From 4e24904ddfcbfdae0874a61d5f998ad50b7f44b2 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 30 Jul 2024 15:03:27 -0700 Subject: [PATCH 01/36] prediction output in model eval mode --- bar.mztab | 189 ++++++++++++++++++++++++++++++++ casanovo/data/datasets.py | 10 +- casanovo/denovo/dataloaders.py | 8 +- casanovo/denovo/model.py | 72 +++++++++--- casanovo/denovo/model_runner.py | 10 +- foo.mztab | 189 ++++++++++++++++++++++++++++++++ 6 files changed, 460 insertions(+), 18 deletions(-) create mode 100644 bar.mztab create mode 100644 foo.mztab diff --git a/bar.mztab b/bar.mztab new file mode 100644 index 00000000..cbcd1bb5 --- /dev/null +++ b/bar.mztab @@ -0,0 +1,189 @@ +MTD mzTab-version 1.0.0 +MTD mzTab-mode Summary +MTD mzTab-type Identification +MTD description Casanovo identification file bar +MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] +MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] +MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] +MTD fixed_mod[1]-site C +MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[1]-site N +MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[2]-site Q +MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] +MTD variable_mod[3]-site M +MTD variable_mod[4] [UNIMOD, UNIMOD:5, Carbamyl, ] +MTD variable_mod[4]-site N-term +MTD variable_mod[5] [UNIMOD, UNIMOD:385, Ammonia-loss, ] +MTD variable_mod[5]-site N-term +MTD variable_mod[6] [UNIMOD, UNIMOD:1, Acetyl, ] +MTD variable_mod[6]-site N-term +MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt +MTD software[1]-setting[2] config_filename = default +MTD software[1]-setting[3] precursor_mass_tol = 50.0 +MTD software[1]-setting[4] isotope_error_range = (0, 1) +MTD software[1]-setting[5] min_peptide_len = 6 +MTD software[1]-setting[6] predict_batch_size = 1024 +MTD software[1]-setting[7] n_beams = 1 +MTD software[1]-setting[8] top_match = 1 +MTD software[1]-setting[9] accelerator = auto +MTD software[1]-setting[10] devices = None +MTD software[1]-setting[11] random_seed = 454 +MTD software[1]-setting[12] n_log = 1 +MTD software[1]-setting[13] tb_summarywriter = None +MTD software[1]-setting[14] save_top_k = 5 +MTD software[1]-setting[15] model_save_folder_path = +MTD software[1]-setting[16] val_check_interval = 50000 +MTD software[1]-setting[17] n_peaks = 150 +MTD software[1]-setting[18] min_mz = 50.0 +MTD software[1]-setting[19] max_mz = 2500.0 +MTD software[1]-setting[20] min_intensity = 0.01 +MTD software[1]-setting[21] remove_precursor_tol = 2.0 +MTD software[1]-setting[22] max_charge = 10 +MTD software[1]-setting[23] dim_model = 512 +MTD software[1]-setting[24] n_head = 8 +MTD software[1]-setting[25] dim_feedforward = 1024 +MTD software[1]-setting[26] n_layers = 9 +MTD software[1]-setting[27] dropout = 0.0 +MTD software[1]-setting[28] dim_intensity = None +MTD software[1]-setting[29] max_length = 100 +MTD software[1]-setting[30] warmup_iters = 100000 +MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 +MTD software[1]-setting[32] learning_rate = 0.0005 +MTD software[1]-setting[33] weight_decay = 1e-05 +MTD software[1]-setting[34] train_label_smoothing = 0.01 +MTD software[1]-setting[35] train_batch_size = 32 +MTD software[1]-setting[36] max_epochs = 30 +MTD software[1]-setting[37] num_sanity_val_steps = 0 +MTD software[1]-setting[38] calculate_precision = False +MTD software[1]-setting[40] n_workers = 0 +MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf +PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores +PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 +PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 +PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 +PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 +PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 +PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 +PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 +PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 +PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 +PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 +PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 +PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 +PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 +PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 +PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 +PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9672952890396118 null null 2 614.33795 614.33821831688 ms_run[1]:index=15 null null null null 0.97399,0.97959,0.97837,0.97845,0.96474,0.84979,0.97928,0.97613,0.97886,0.97760,0.97960,0.97994 +PSM LQEEERER 17 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.975036793284946 null null 2 544.77 544.77017681688 ms_run[1]:index=16 null null null null 0.91222,0.98079,0.98579,0.98252,0.98429,0.98225,0.98285,0.98220 +PSM TRGHESEMK 18 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1844959855079651 null null 2 539.25323 537.75346831688 ms_run[1]:index=17 null null null null 0.90297,0.90465,0.82135,0.90041,0.64139,0.62194,0.66087,0.89718,0.90124 +PSM +42.011KVEDPPRK 19 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.24581749439239498 null null 2 507.26154 505.78509881688007 ms_run[1]:index=18 null null null null 0.77158,0.66196,0.86775,0.87090,0.70578,0.61787,0.85217,0.69678,0.62489 +PSM TESPAEGKQEEEK 20 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.868788189121655 null null 2 731.3395 731.3388133168802 ms_run[1]:index=19 null null null null 0.92347,0.91621,0.74657,0.61987,0.87546,0.65200,0.92947,0.92629,0.93151,0.92995,0.92921,0.92534,0.92826 +PSM LVEEETKK 21 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879584113756815 null null 2 488.27112 488.27148531688005 ms_run[1]:index=20 null null null null 0.98623,0.98691,0.98852,0.98742,0.98734,0.98694,0.99077,0.98849 +PSM KAETLGEK 22 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9864536391364204 null null 2 438.24524 438.24527081688 ms_run[1]:index=21 null null null null 0.98740,0.98704,0.98770,0.98844,0.98931,0.98661,0.98774,0.97524 +PSM C+57.021LKPNETK 23 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9895809359020658 null null 2 495.25775 495.25785531688 ms_run[1]:index=22 null null null null 0.98927,0.98929,0.98595,0.99043,0.99001,0.99081,0.98784,0.99231 +PSM GHQALER 24 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9861482679843903 null null 2 405.71454 405.71447681688 ms_run[1]:index=23 null null null null 0.98369,0.97763,0.98807,0.98786,0.98838,0.98693,0.98818 +PSM TNNLRPK 25 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9859854802489281 null null 2 421.74548 421.74577181688005 ms_run[1]:index=24 null null null null 0.98893,0.99008,0.98974,0.98259,0.98795,0.97375,0.98633 +PSM +43.006DTPGHATPGHGAGTQER 26 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.22608531070382976 null null 2 867.40045 866.39330131688 ms_run[1]:index=25 null null null null 0.85561,0.57927,0.49126,0.50495,0.70489,0.76038,0.75372,0.53050,0.87917,0.87740,0.88139,0.87799,0.88406,0.88016,0.88217,0.87672,0.82864,0.77355 +PSM KSYTTPK 27 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8933427818119526 null null 2 412.72778 412.72925231688004 ms_run[1]:index=26 null null null null 0.93932,0.94376,0.93479,0.61684,0.94099,0.93574,0.89386 +PSM VLEGHAEK 28 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879539277818468 null null 2 441.73788 441.73761731688 ms_run[1]:index=27 null null null null 0.98716,0.98573,0.98970,0.98983,0.98921,0.98323,0.98926,0.98847 +PSM LQHEATAATQK 29 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9673882275819778 null null 2 599.3142 599.31474381688 ms_run[1]:index=28 null null null null 0.97810,0.97690,0.97761,0.96875,0.88905,0.98107,0.97901,0.94171,0.98001,0.97853,0.97914 +PSM KEAPAPPK 30 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.99110433128145 null null 2 419.24496 419.24507831688004 ms_run[1]:index=29 null null null null 0.98966,0.99341,0.99059,0.99097,0.99120,0.99191,0.99078,0.99143 +PSM ERDELR 31 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9874146069799151 null null 2 409.2106 409.2117663168801 ms_run[1]:index=30 null null null null 0.98921,0.98706,0.98802,0.98241,0.98891,0.98739 +PSM EVLHANNR 32 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8818797965844473 null null 2 476.75156 476.75158981687997 ms_run[1]:index=31 null null null null 0.93772,0.73514,0.67541,0.93265,0.93705,0.93603,0.93502,0.91176 +PSM NNTLTPNKPNK 33 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1514618446429571 null null 2 613.8276 620.83584181688 ms_run[1]:index=32 null null null null 0.90068,0.80453,0.91917,0.67357,0.80102,0.91849,0.91801,0.71365,0.91622,0.90961,0.78907 +PSM MQEHMR 34 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894828966685704 null null 2 416.18372 416.18364081688 ms_run[1]:index=33 null null null null 0.98712,0.98906,0.99189,0.98772,0.99073,0.98986 +PSM HNSYTAC+57.021ETHK 35 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8552879715959231 null null 2 674.29083 674.29094231688 ms_run[1]:index=34 null null null null 0.91161,0.92276,0.92215,0.75983,0.57698,0.64840,0.90726,0.92049,0.92356,0.92284,0.92449 +PSM WAPGHATPFSDESSSR 36 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43844590730526867 null null 2 867.4 866.3897028168802 ms_run[1]:index=35 null null null null 0.62368,0.35030,0.34498,0.43399,0.63293,0.39463,0.54277,0.45963,0.77829,0.76285,0.61244,0.56565,0.66891,0.77050,0.38220,0.45175 +PSM GDDETLHK 37 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9814771148893568 null null 2 457.71384 457.71433481688 ms_run[1]:index=36 null null null null 0.98366,0.98677,0.98606,0.98567,0.97685,0.97706,0.96534,0.98540 +PSM NEKSEEEQSSASVK 38 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9875149647394816 null null 2 776.35913 776.3602803168801 ms_run[1]:index=37 null null null null 0.98915,0.98944,0.98834,0.98835,0.98850,0.98888,0.97847,0.98778,0.98852,0.98666,0.98830,0.98710,0.98650,0.98822 +PSM NNTVTPGGKPGGK 39 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.946726496730532 null null 2 613.82745 613.8280178168801 ms_run[1]:index=38 null null null null 0.93242,0.80678,0.95406,0.96786,0.88768,0.96598,0.96954,0.96820,0.96772,0.96757,0.96759,0.96293,0.96766 +PSM HNGEEEEETHK 40 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.4023066883285841 null null 2 674.2913 669.7814653168799 ms_run[1]:index=39 null null null null 0.79198,0.79514,0.76636,0.39427,0.42610,0.40046,0.40083,0.39425,0.44152,0.77926,0.78835 +PSM HDSVEER 41 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9554774761199951 null null 2 436.19864 436.1988558168801 ms_run[1]:index=40 null null null null 0.94772,0.95530,0.92708,0.94280,0.96933,0.95420,0.97425 +PSM EGGQVASMEEEK 42 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.48210483216322386 null null 2 648.29266 647.28499981688 ms_run[1]:index=41 null null null null 0.39005,0.43086,0.42453,0.34300,0.64313,0.48547,0.75237,0.73883,0.36843,0.39590,0.47632,0.52967 +PSM AVTKYTSSK 43 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865922451019287 null null 2 492.77188 492.77164831688003 ms_run[1]:index=42 null null null null 0.98637,0.98900,0.98957,0.98818,0.98921,0.98818,0.98726,0.97004,0.98958 +PSM TKYTSSK 44 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.977924220263958 null null 2 407.71896 407.71888431688 ms_run[1]:index=43 null null null null 0.98495,0.98298,0.98361,0.98325,0.98555,0.93525,0.98402 +PSM SSFSQHAR 45 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9911030067337884 null null 2 460.22247 460.22266531687995 ms_run[1]:index=44 null null null null 0.99131,0.99140,0.99089,0.99075,0.99078,0.99212,0.99089,0.99124 +PSM SYTSSDTAHK 46 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8599473617293618 null null 2 548.73834 548.7489013168799 ms_run[1]:index=45 null null null null 0.92316,0.92249,0.69404,0.88593,0.67066,0.74161,0.92698,0.92628,0.91877,0.92507 +PSM GTGHTDAENEEVK 47 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6680682482463973 null null 2 693.80896 693.81021881688 ms_run[1]:index=46 null null null null 0.82323,0.80847,0.54724,0.46113,0.45871,0.66241,0.80819,0.56945,0.81953,0.69455,0.49138,0.58402,0.79585 +PSM 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ms_run[1]:index=97 null null null null 0.98951,0.98664,0.98892,0.98538,0.98991,0.98926,0.99082 +PSM SGTATAANPAEM+15.995YK 99 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6758072773615519 null null 2 714.3115 714.32719081688 ms_run[1]:index=98 null null null null 0.49935,0.43461,0.57078,0.53960,0.56327,0.81141,0.63182,0.67101,0.83289,0.79074,0.74597,0.62813,0.74957,0.83457 +PSM +42.011SGEELRK 100 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.15170641077889335 null null 2 437.25616 430.7272493168801 ms_run[1]:index=99 null null null null 0.85811,0.91444,0.88994,0.69713,0.91029,0.88104,0.68493,0.87894 +PSM TSYAQHQQVR 101 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.989588509906422 null null 2 609.3046 609.3047148168799 ms_run[1]:index=100 null null null null 0.99056,0.99011,0.98729,0.98997,0.99053,0.98848,0.98996,0.98965,0.99105,0.98859 +PSM NDEELNK 102 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9784338027238846 null null 2 431.2012 431.20106381688004 ms_run[1]:index=101 null null null null 0.98508,0.98284,0.98438,0.97530,0.97293,0.96303,0.97950 +PSM GGSLPQNHLHGH 103 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7780202948130094 null null 2 627.3102 627.3103353168799 ms_run[1]:index=102 null null null null 0.88073,0.88552,0.88639,0.53989,0.48982,0.59155,0.75677,0.88470,0.79813,0.81800,0.81249,0.88578 +PSM EESGKPQHVTVK 104 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9577845564255347 null null 2 669.8538 669.85423681688 ms_run[1]:index=103 null null null null 0.97224,0.97328,0.97316,0.97085,0.97283,0.78519,0.97378,0.96353,0.97323,0.97306,0.97223,0.97381 +PSM NSYTN+0.984GHSSDK 105 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6759249443809191 null null 2 605.7616 605.75217631688 ms_run[1]:index=104 null null null null 0.80744,0.47209,0.48691,0.43885,0.55379,0.57064,0.61858,0.83322,0.82685,0.83470,0.83499 +PSM APTQGEC+57.021HC+57.021DQTF 106 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6652015820145607 null null 2 775.8415 775.8035578168799 ms_run[1]:index=105 null null null null 0.42189,0.79374,0.76732,0.44555,0.50619,0.52009,0.46332,0.59417,0.82448,0.66210,0.82893,0.82902,0.82790 +PSM NVHELEK 107 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9881609752774239 null null 2 434.7295 434.72979181688004 ms_run[1]:index=106 null null null null 0.98844,0.98742,0.98892,0.98666,0.98955,0.98984,0.98553 +PSM YPNHSVDR 108 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9701713191138374 null null 2 494.2362 494.23577281688 ms_run[1]:index=107 null null null null 0.98136,0.88748,0.97896,0.98037,0.98181,0.97936,0.98056,0.98167 +PSM NKEGEVDYAK 109 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8123747543855147 null null 2 576.78033 576.7802103168799 ms_run[1]:index=108 null null null null 0.90083,0.90001,0.89895,0.59818,0.57671,0.56759,0.90301,0.89488,0.90020,0.89448 +PSM LRPEPNTGK 110 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.052142149209976174 null null 2 499.27567 506.28271881688005 ms_run[1]:index=109 null null null null 0.96482,0.96376,0.96742,0.96250,0.96909,0.84115,0.96040,0.94795,0.93244 +PSM NN+0.984EELNK 111 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20876559987664223 null null 2 421.71188 431.20106381688004 ms_run[1]:index=110 null null null null 0.89154,0.89164,0.89013,0.88795,0.88142,0.61297,0.87860 +PSM PHESNYEEDGK 112 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3362173897524675 null null 2 646.7648 652.77311331688 ms_run[1]:index=111 null null null null 0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 +PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 +PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 +PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 +PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 +PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 +PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 +PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 +PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 +PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 +PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 +PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 +PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 +PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 +PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 +PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 +PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 diff --git a/casanovo/data/datasets.py b/casanovo/data/datasets.py index 6244e88f..f7b2fe7e 100644 --- a/casanovo/data/datasets.py +++ b/casanovo/data/datasets.py @@ -87,6 +87,7 @@ def __getitem__( spectrum = self._process_peaks( mz_array, int_array, precursor_mz, precursor_charge ) + return ( spectrum, precursor_mz, @@ -264,4 +265,11 @@ def __getitem__(self, idx: int) -> Tuple[torch.Tensor, float, int, str]: spectrum = self._process_peaks( mz_array, int_array, precursor_mz, precursor_charge ) - return spectrum, precursor_mz, precursor_charge, peptide + + return ( + spectrum, + precursor_mz, + precursor_charge, + self.get_spectrum_id(idx), + peptide, + ) diff --git a/casanovo/denovo/dataloaders.py b/casanovo/denovo/dataloaders.py index fe5d6237..ba58d83c 100644 --- a/casanovo/denovo/dataloaders.py +++ b/casanovo/denovo/dataloaders.py @@ -202,7 +202,11 @@ def prepare_batch( The spectrum identifiers (during de novo sequencing) or peptide sequences (during training). """ - spectra, precursor_mzs, precursor_charges, spectrum_ids = list(zip(*batch)) + batch_list = list(zip(*batch)) + spectra, precursor_mzs, precursor_charges, spectrum_ids = batch_list[0:4] + peptide_sequence = ( + None if len(batch_list) <= 4 else np.asarray(batch_list[4]) + ) spectra = torch.nn.utils.rnn.pad_sequence(spectra, batch_first=True) precursor_mzs = torch.tensor(precursor_mzs) precursor_charges = torch.tensor(precursor_charges) @@ -210,4 +214,4 @@ def prepare_batch( precursors = torch.vstack( [precursor_masses, precursor_charges, precursor_mzs] ).T.float() - return spectra, precursors, np.asarray(spectrum_ids) + return spectra, precursors, np.asarray(spectrum_ids), peptide_sequence diff --git a/casanovo/denovo/model.py b/casanovo/denovo/model.py index 77df6df5..29acaf40 100644 --- a/casanovo/denovo/model.py +++ b/casanovo/denovo/model.py @@ -748,7 +748,7 @@ def training_step( torch.Tensor The loss of the training step. """ - pred, truth = self._forward_step(*batch) + pred, truth = self._forward_step(batch[0], batch[1], batch[3]) pred = pred[:, :-1, :].reshape(-1, self.decoder.vocab_size + 1) if mode == "train": loss = self.celoss(pred, truth.flatten()) @@ -781,14 +781,15 @@ def validation_step( The loss of the validation step. """ # Record the loss. + forward_step = self.forward(batch[0], batch[1]) loss = self.training_step(batch, mode="valid") if not self.calculate_precision: - return loss + return loss, self._get_predictions(batch, forward_step) # Calculate and log amino acid and peptide match evaluation metrics from # the predicted peptides. peptides_pred, peptides_true = [], batch[2] - for spectrum_preds in self.forward(batch[0], batch[1]): + for spectrum_preds in forward_step: for _, _, pred in spectrum_preds: peptides_pred.append(pred) @@ -810,26 +811,35 @@ def validation_step( aa_precision, **log_args, ) - return loss + return loss, self._get_predictions(batch, forward_step) - def predict_step( - self, batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], *args + def _get_predictions( + self, + batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], + forward_res: List[List[Tuple[float, np.ndarray, str]]], ) -> List[Tuple[np.ndarray, float, float, str, float, np.ndarray]]: """ - A single prediction step. + Extract predictions from model output for a batch of spectra. + + Processes the output from a forward pass of the model to + generate a list of predictions for each spectrum in the batch. Parameters ---------- batch : Tuple[torch.Tensor, torch.Tensor, torch.Tensor] - A batch of (i) MS/MS spectra, (ii) precursor information, (iii) - spectrum identifiers as torch Tensors. + A tuple containing: + - (i) MS/MS spectra data as a torch.Tensor. + - (ii) Precursor information, including charge and m/z values, + - (iii) Spectrum identifiers as a torch.Tensor. + forward_res : List[List[Tuple[float, np.ndarray, str]]] + Output from forward_step Returns ------- - predictions: List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] - Model predictions for the given batch of spectra containing spectrum - ids, precursor information, peptide sequences as well as peptide - and amino acid-level confidence scores. + List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] + Model predictions for the given batch of spectra containing + spectrum ids, precursor information, peptide sequences as well as + peptide and amino acid-level confidence scores. """ predictions = [] for ( @@ -841,7 +851,7 @@ def predict_step( batch[1][:, 1].cpu().detach().numpy(), batch[1][:, 2].cpu().detach().numpy(), batch[2], - self.forward(batch[0], batch[1]), + forward_res, ): for peptide_score, aa_scores, peptide in spectrum_preds: predictions.append( @@ -857,6 +867,27 @@ def predict_step( return predictions + def predict_step( + self, batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], *args + ) -> List[Tuple[np.ndarray, float, float, str, float, np.ndarray]]: + """ + A single prediction step. + + Parameters + ---------- + batch : Tuple[torch.Tensor, torch.Tensor, torch.Tensor] + A batch of (i) MS/MS spectra, (ii) precursor information, (iii) + spectrum identifiers as torch Tensors. + + Returns + ------- + predictions: List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] + Model predictions for the given batch of spectra containing spectrum + ids, precursor information, peptide sequences as well as peptide + and amino acid-level confidence scores. + """ + return self._get_predictions(batch, self.forward(batch[0], batch[1])) + def on_train_epoch_end(self) -> None: """ Log the training loss at the end of each epoch. @@ -925,6 +956,19 @@ def on_predict_batch_end( ), ) + def on_validation_batch_end( + self, + outputs: Tuple[ + torch.Tensor, List[Tuple[np.ndarray, List[str], torch.Tensor]] + ], + *args, + ) -> None: + """ + Write the predicted peptide sequences and amino acid scores to the + output file. + """ + self.on_predict_batch_end(outputs[1]) + def _log_history(self) -> None: """ Write log to console, if requested. diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index d5acacb3..0914db20 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -128,13 +128,21 @@ def evaluate(self, peak_path: Iterable[str]) -> None: ------- self """ + self.writer = ms_io.MztabWriter(Path("foo.mztab")) + self.writer.set_metadata( + self.config, + model=str(self.model_filename), + config_filename=self.config.file, + ) + self.initialize_trainer(train=False) self.initialize_model(train=False) + self.model.out_writer = self.writer test_index = self._get_index(peak_path, True, "evaluation") + self.writer.set_ms_run(test_index.ms_files) self.initialize_data_module(test_index=test_index) self.loaders.setup(stage="test", annotated=True) - self.trainer.validate(self.model, self.loaders.test_dataloader()) def predict(self, peak_path: Iterable[str], output: str) -> None: diff --git a/foo.mztab b/foo.mztab new file mode 100644 index 00000000..aa8a6922 --- /dev/null +++ b/foo.mztab @@ -0,0 +1,189 @@ +MTD mzTab-version 1.0.0 +MTD mzTab-mode Summary +MTD mzTab-type Identification +MTD description Casanovo identification file foo +MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] +MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] +MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] +MTD fixed_mod[1]-site C +MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[1]-site N +MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[2]-site Q +MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] +MTD variable_mod[3]-site M +MTD variable_mod[4] [UNIMOD, UNIMOD:5, Carbamyl, ] +MTD variable_mod[4]-site N-term +MTD variable_mod[5] [UNIMOD, UNIMOD:1, Acetyl, ] +MTD variable_mod[5]-site N-term +MTD variable_mod[6] [UNIMOD, UNIMOD:385, Ammonia-loss, ] +MTD variable_mod[6]-site N-term +MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt +MTD software[1]-setting[2] config_filename = default +MTD software[1]-setting[3] precursor_mass_tol = 50.0 +MTD software[1]-setting[4] isotope_error_range = (0, 1) +MTD software[1]-setting[5] min_peptide_len = 6 +MTD software[1]-setting[6] predict_batch_size = 1024 +MTD software[1]-setting[7] n_beams = 1 +MTD software[1]-setting[8] top_match = 1 +MTD software[1]-setting[9] accelerator = auto +MTD software[1]-setting[10] devices = None +MTD software[1]-setting[11] random_seed = 454 +MTD software[1]-setting[12] n_log = 1 +MTD software[1]-setting[13] tb_summarywriter = None +MTD software[1]-setting[14] save_top_k = 5 +MTD software[1]-setting[15] model_save_folder_path = +MTD software[1]-setting[16] val_check_interval = 50000 +MTD software[1]-setting[17] n_peaks = 150 +MTD software[1]-setting[18] min_mz = 50.0 +MTD software[1]-setting[19] max_mz = 2500.0 +MTD software[1]-setting[20] min_intensity = 0.01 +MTD software[1]-setting[21] remove_precursor_tol = 2.0 +MTD software[1]-setting[22] max_charge = 10 +MTD software[1]-setting[23] dim_model = 512 +MTD software[1]-setting[24] n_head = 8 +MTD software[1]-setting[25] dim_feedforward = 1024 +MTD software[1]-setting[26] n_layers = 9 +MTD software[1]-setting[27] dropout = 0.0 +MTD software[1]-setting[28] dim_intensity = None +MTD software[1]-setting[29] max_length = 100 +MTD software[1]-setting[30] warmup_iters = 100000 +MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 +MTD software[1]-setting[32] learning_rate = 0.0005 +MTD software[1]-setting[33] weight_decay = 1e-05 +MTD software[1]-setting[34] train_label_smoothing = 0.01 +MTD software[1]-setting[35] train_batch_size = 32 +MTD software[1]-setting[36] max_epochs = 30 +MTD software[1]-setting[37] num_sanity_val_steps = 0 +MTD software[1]-setting[38] calculate_precision = False +MTD software[1]-setting[40] n_workers = 0 +MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf +PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores +PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 +PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 +PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 +PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 +PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 +PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 +PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 +PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 +PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 +PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 +PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 +PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 +PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 +PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 +PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 +PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9672952890396118 null null 2 614.33795 614.33821831688 ms_run[1]:index=15 null null null null 0.97399,0.97959,0.97837,0.97845,0.96474,0.84979,0.97928,0.97613,0.97886,0.97760,0.97960,0.97994 +PSM LQEEERER 17 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.975036793284946 null null 2 544.77 544.77017681688 ms_run[1]:index=16 null null null null 0.91222,0.98079,0.98579,0.98252,0.98429,0.98225,0.98285,0.98220 +PSM TRGHESEMK 18 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1844959855079651 null null 2 539.25323 537.75346831688 ms_run[1]:index=17 null null null null 0.90297,0.90465,0.82135,0.90041,0.64139,0.62194,0.66087,0.89718,0.90124 +PSM +42.011KVEDPPRK 19 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.24581749439239498 null null 2 507.26154 505.78509881688007 ms_run[1]:index=18 null null null null 0.77158,0.66196,0.86775,0.87090,0.70578,0.61787,0.85217,0.69678,0.62489 +PSM TESPAEGKQEEEK 20 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.868788189121655 null null 2 731.3395 731.3388133168802 ms_run[1]:index=19 null null null null 0.92347,0.91621,0.74657,0.61987,0.87546,0.65200,0.92947,0.92629,0.93151,0.92995,0.92921,0.92534,0.92826 +PSM LVEEETKK 21 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879584113756815 null null 2 488.27112 488.27148531688005 ms_run[1]:index=20 null null null null 0.98623,0.98691,0.98852,0.98742,0.98734,0.98694,0.99077,0.98849 +PSM KAETLGEK 22 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9864536391364204 null null 2 438.24524 438.24527081688 ms_run[1]:index=21 null null null null 0.98740,0.98704,0.98770,0.98844,0.98931,0.98661,0.98774,0.97524 +PSM C+57.021LKPNETK 23 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9895809359020658 null null 2 495.25775 495.25785531688 ms_run[1]:index=22 null null null null 0.98927,0.98929,0.98595,0.99043,0.99001,0.99081,0.98784,0.99231 +PSM GHQALER 24 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9861482679843903 null null 2 405.71454 405.71447681688 ms_run[1]:index=23 null null null null 0.98369,0.97763,0.98807,0.98786,0.98838,0.98693,0.98818 +PSM TNNLRPK 25 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9859854802489281 null null 2 421.74548 421.74577181688005 ms_run[1]:index=24 null null null null 0.98893,0.99008,0.98974,0.98259,0.98795,0.97375,0.98633 +PSM +43.006DTPGHATPGHGAGTQER 26 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.22608531070382976 null null 2 867.40045 866.39330131688 ms_run[1]:index=25 null null null null 0.85561,0.57927,0.49126,0.50495,0.70489,0.76038,0.75372,0.53050,0.87917,0.87740,0.88139,0.87799,0.88406,0.88016,0.88217,0.87672,0.82864,0.77355 +PSM KSYTTPK 27 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8933427818119526 null null 2 412.72778 412.72925231688004 ms_run[1]:index=26 null null null null 0.93932,0.94376,0.93479,0.61684,0.94099,0.93574,0.89386 +PSM VLEGHAEK 28 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879539277818468 null null 2 441.73788 441.73761731688 ms_run[1]:index=27 null null null null 0.98716,0.98573,0.98970,0.98983,0.98921,0.98323,0.98926,0.98847 +PSM LQHEATAATQK 29 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9673882275819778 null null 2 599.3142 599.31474381688 ms_run[1]:index=28 null null null null 0.97810,0.97690,0.97761,0.96875,0.88905,0.98107,0.97901,0.94171,0.98001,0.97853,0.97914 +PSM KEAPAPPK 30 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.99110433128145 null null 2 419.24496 419.24507831688004 ms_run[1]:index=29 null null null null 0.98966,0.99341,0.99059,0.99097,0.99120,0.99191,0.99078,0.99143 +PSM ERDELR 31 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9874146069799151 null null 2 409.2106 409.2117663168801 ms_run[1]:index=30 null null null null 0.98921,0.98706,0.98802,0.98241,0.98891,0.98739 +PSM EVLHANNR 32 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8818797965844473 null null 2 476.75156 476.75158981687997 ms_run[1]:index=31 null null null null 0.93772,0.73514,0.67541,0.93265,0.93705,0.93603,0.93502,0.91176 +PSM NNTLTPNKPNK 33 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1514618446429571 null null 2 613.8276 620.83584181688 ms_run[1]:index=32 null null null null 0.90068,0.80453,0.91917,0.67357,0.80102,0.91849,0.91801,0.71365,0.91622,0.90961,0.78907 +PSM MQEHMR 34 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894828966685704 null null 2 416.18372 416.18364081688 ms_run[1]:index=33 null null null null 0.98712,0.98906,0.99189,0.98772,0.99073,0.98986 +PSM HNSYTAC+57.021ETHK 35 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8552879715959231 null null 2 674.29083 674.29094231688 ms_run[1]:index=34 null null null null 0.91161,0.92276,0.92215,0.75983,0.57698,0.64840,0.90726,0.92049,0.92356,0.92284,0.92449 +PSM WAPGHATPFSDESSSR 36 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43844590730526867 null null 2 867.4 866.3897028168802 ms_run[1]:index=35 null null null null 0.62368,0.35030,0.34498,0.43399,0.63293,0.39463,0.54277,0.45963,0.77829,0.76285,0.61244,0.56565,0.66891,0.77050,0.38220,0.45175 +PSM GDDETLHK 37 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9814771148893568 null null 2 457.71384 457.71433481688 ms_run[1]:index=36 null null null null 0.98366,0.98677,0.98606,0.98567,0.97685,0.97706,0.96534,0.98540 +PSM NEKSEEEQSSASVK 38 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9875149647394816 null null 2 776.35913 776.3602803168801 ms_run[1]:index=37 null null null null 0.98915,0.98944,0.98834,0.98835,0.98850,0.98888,0.97847,0.98778,0.98852,0.98666,0.98830,0.98710,0.98650,0.98822 +PSM NNTVTPGGKPGGK 39 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.946726496730532 null null 2 613.82745 613.8280178168801 ms_run[1]:index=38 null null null null 0.93242,0.80678,0.95406,0.96786,0.88768,0.96598,0.96954,0.96820,0.96772,0.96757,0.96759,0.96293,0.96766 +PSM HNGEEEEETHK 40 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.4023066883285841 null null 2 674.2913 669.7814653168799 ms_run[1]:index=39 null null null null 0.79198,0.79514,0.76636,0.39427,0.42610,0.40046,0.40083,0.39425,0.44152,0.77926,0.78835 +PSM HDSVEER 41 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9554774761199951 null null 2 436.19864 436.1988558168801 ms_run[1]:index=40 null null null null 0.94772,0.95530,0.92708,0.94280,0.96933,0.95420,0.97425 +PSM EGGQVASMEEEK 42 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.48210483216322386 null null 2 648.29266 647.28499981688 ms_run[1]:index=41 null null null null 0.39005,0.43086,0.42453,0.34300,0.64313,0.48547,0.75237,0.73883,0.36843,0.39590,0.47632,0.52967 +PSM AVTKYTSSK 43 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865922451019287 null null 2 492.77188 492.77164831688003 ms_run[1]:index=42 null null null null 0.98637,0.98900,0.98957,0.98818,0.98921,0.98818,0.98726,0.97004,0.98958 +PSM TKYTSSK 44 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.977924220263958 null null 2 407.71896 407.71888431688 ms_run[1]:index=43 null null null null 0.98495,0.98298,0.98361,0.98325,0.98555,0.93525,0.98402 +PSM SSFSQHAR 45 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9911030067337884 null null 2 460.22247 460.22266531687995 ms_run[1]:index=44 null null null null 0.99131,0.99140,0.99089,0.99075,0.99078,0.99212,0.99089,0.99124 +PSM SYTSSDTAHK 46 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8599473617293618 null null 2 548.73834 548.7489013168799 ms_run[1]:index=45 null null null null 0.92316,0.92249,0.69404,0.88593,0.67066,0.74161,0.92698,0.92628,0.91877,0.92507 +PSM GTGHTDAENEEVK 47 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6680682482463973 null null 2 693.80896 693.81021881688 ms_run[1]:index=46 null null null null 0.82323,0.80847,0.54724,0.46113,0.45871,0.66241,0.80819,0.56945,0.81953,0.69455,0.49138,0.58402,0.79585 +PSM NEKSEETTEEEVK 48 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7301746702619961 null null 2 776.3595 776.3546553168801 ms_run[1]:index=47 null null null null 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0.98951,0.98664,0.98892,0.98538,0.98991,0.98926,0.99082 +PSM SGTATAANPAEM+15.995YK 99 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6758072773615519 null null 2 714.3115 714.32719081688 ms_run[1]:index=98 null null null null 0.49935,0.43461,0.57078,0.53960,0.56327,0.81141,0.63182,0.67101,0.83289,0.79074,0.74597,0.62813,0.74957,0.83457 +PSM +42.011SGEELRK 100 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.15170641077889335 null null 2 437.25616 430.7272493168801 ms_run[1]:index=99 null null null null 0.85811,0.91444,0.88994,0.69713,0.91029,0.88104,0.68493,0.87894 +PSM TSYAQHQQVR 101 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.989588509906422 null null 2 609.3046 609.3047148168799 ms_run[1]:index=100 null null null null 0.99056,0.99011,0.98729,0.98997,0.99053,0.98848,0.98996,0.98965,0.99105,0.98859 +PSM NDEELNK 102 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9784338027238846 null null 2 431.2012 431.20106381688004 ms_run[1]:index=101 null null null null 0.98508,0.98284,0.98438,0.97530,0.97293,0.96303,0.97950 +PSM GGSLPQNHLHGH 103 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7780202948130094 null null 2 627.3102 627.3103353168799 ms_run[1]:index=102 null null null null 0.88073,0.88552,0.88639,0.53989,0.48982,0.59155,0.75677,0.88470,0.79813,0.81800,0.81249,0.88578 +PSM EESGKPQHVTVK 104 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9577845564255347 null null 2 669.8538 669.85423681688 ms_run[1]:index=103 null null null null 0.97224,0.97328,0.97316,0.97085,0.97283,0.78519,0.97378,0.96353,0.97323,0.97306,0.97223,0.97381 +PSM NSYTN+0.984GHSSDK 105 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6759249443809191 null null 2 605.7616 605.75217631688 ms_run[1]:index=104 null null null null 0.80744,0.47209,0.48691,0.43885,0.55379,0.57064,0.61858,0.83322,0.82685,0.83470,0.83499 +PSM APTQGEC+57.021HC+57.021DQTF 106 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6652015820145607 null null 2 775.8415 775.8035578168799 ms_run[1]:index=105 null null null null 0.42189,0.79374,0.76732,0.44555,0.50619,0.52009,0.46332,0.59417,0.82448,0.66210,0.82893,0.82902,0.82790 +PSM NVHELEK 107 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9881609752774239 null null 2 434.7295 434.72979181688004 ms_run[1]:index=106 null null null null 0.98844,0.98742,0.98892,0.98666,0.98955,0.98984,0.98553 +PSM YPNHSVDR 108 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9701713191138374 null null 2 494.2362 494.23577281688 ms_run[1]:index=107 null null null null 0.98136,0.88748,0.97896,0.98037,0.98181,0.97936,0.98056,0.98167 +PSM NKEGEVDYAK 109 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8123747543855147 null null 2 576.78033 576.7802103168799 ms_run[1]:index=108 null null null null 0.90083,0.90001,0.89895,0.59818,0.57671,0.56759,0.90301,0.89488,0.90020,0.89448 +PSM LRPEPNTGK 110 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.052142149209976174 null null 2 499.27567 506.28271881688005 ms_run[1]:index=109 null null null null 0.96482,0.96376,0.96742,0.96250,0.96909,0.84115,0.96040,0.94795,0.93244 +PSM NN+0.984EELNK 111 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20876559987664223 null null 2 421.71188 431.20106381688004 ms_run[1]:index=110 null null null null 0.89154,0.89164,0.89013,0.88795,0.88142,0.61297,0.87860 +PSM PHESNYEEDGK 112 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3362173897524675 null null 2 646.7648 652.77311331688 ms_run[1]:index=111 null null null null 0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 +PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 +PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 +PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 +PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 +PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 +PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 +PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 +PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 +PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 +PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 +PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 +PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 +PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 +PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 +PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 +PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 From 82018cff5dbdacb03c297baa9e4822df96430f84 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 30 Jul 2024 15:22:11 -0700 Subject: [PATCH 02/36] eliminate eval command, introduce -e flag for predict command --- bar2.mztab | 189 ++++++++++++++++++++++++++++++++ casanovo/casanovo.py | 48 +++----- casanovo/denovo/model_runner.py | 49 +++------ foo2.mztab | 189 ++++++++++++++++++++++++++++++++ 4 files changed, 408 insertions(+), 67 deletions(-) create mode 100644 bar2.mztab create mode 100644 foo2.mztab diff --git a/bar2.mztab b/bar2.mztab new file mode 100644 index 00000000..78f5939c --- /dev/null +++ b/bar2.mztab @@ -0,0 +1,189 @@ +MTD mzTab-version 1.0.0 +MTD mzTab-mode Summary +MTD mzTab-type Identification +MTD description Casanovo identification file bar2 +MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] +MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] +MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] +MTD fixed_mod[1]-site C +MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[1]-site N +MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[2]-site Q +MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] +MTD variable_mod[3]-site M +MTD variable_mod[4] [UNIMOD, UNIMOD:385, Ammonia-loss, ] +MTD variable_mod[4]-site N-term +MTD variable_mod[5] [UNIMOD, UNIMOD:5, Carbamyl, ] +MTD variable_mod[5]-site N-term +MTD variable_mod[6] [UNIMOD, UNIMOD:1, Acetyl, ] +MTD variable_mod[6]-site N-term +MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt +MTD software[1]-setting[2] config_filename = default +MTD software[1]-setting[3] precursor_mass_tol = 50.0 +MTD software[1]-setting[4] isotope_error_range = (0, 1) +MTD software[1]-setting[5] min_peptide_len = 6 +MTD software[1]-setting[6] predict_batch_size = 1024 +MTD software[1]-setting[7] n_beams = 1 +MTD software[1]-setting[8] top_match = 1 +MTD software[1]-setting[9] accelerator = auto +MTD software[1]-setting[10] devices = None +MTD software[1]-setting[11] random_seed = 454 +MTD software[1]-setting[12] n_log = 1 +MTD software[1]-setting[13] tb_summarywriter = None +MTD software[1]-setting[14] save_top_k = 5 +MTD software[1]-setting[15] model_save_folder_path = +MTD software[1]-setting[16] val_check_interval = 50000 +MTD software[1]-setting[17] n_peaks = 150 +MTD software[1]-setting[18] min_mz = 50.0 +MTD software[1]-setting[19] max_mz = 2500.0 +MTD software[1]-setting[20] min_intensity = 0.01 +MTD software[1]-setting[21] remove_precursor_tol = 2.0 +MTD software[1]-setting[22] max_charge = 10 +MTD software[1]-setting[23] dim_model = 512 +MTD software[1]-setting[24] n_head = 8 +MTD software[1]-setting[25] dim_feedforward = 1024 +MTD software[1]-setting[26] n_layers = 9 +MTD software[1]-setting[27] dropout = 0.0 +MTD software[1]-setting[28] dim_intensity = None +MTD software[1]-setting[29] max_length = 100 +MTD software[1]-setting[30] warmup_iters = 100000 +MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 +MTD software[1]-setting[32] learning_rate = 0.0005 +MTD software[1]-setting[33] weight_decay = 1e-05 +MTD software[1]-setting[34] train_label_smoothing = 0.01 +MTD software[1]-setting[35] train_batch_size = 32 +MTD software[1]-setting[36] max_epochs = 30 +MTD software[1]-setting[37] num_sanity_val_steps = 0 +MTD software[1]-setting[38] calculate_precision = False +MTD software[1]-setting[40] n_workers = 0 +MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf +PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores +PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 +PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 +PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 +PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 +PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 +PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 +PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 +PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 +PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 +PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 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MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9673882275819778 null null 2 599.3142 599.31474381688 ms_run[1]:index=28 null null null null 0.97810,0.97690,0.97761,0.96875,0.88905,0.98107,0.97901,0.94171,0.98001,0.97853,0.97914 +PSM KEAPAPPK 30 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.99110433128145 null null 2 419.24496 419.24507831688004 ms_run[1]:index=29 null null null null 0.98966,0.99341,0.99059,0.99097,0.99120,0.99191,0.99078,0.99143 +PSM ERDELR 31 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9874146069799151 null null 2 409.2106 409.2117663168801 ms_run[1]:index=30 null null null null 0.98921,0.98706,0.98802,0.98241,0.98891,0.98739 +PSM EVLHANNR 32 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8818797965844473 null null 2 476.75156 476.75158981687997 ms_run[1]:index=31 null null null null 0.93772,0.73514,0.67541,0.93265,0.93705,0.93603,0.93502,0.91176 +PSM NNTLTPNKPNK 33 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1514618446429571 null null 2 613.8276 620.83584181688 ms_run[1]:index=32 null null null null 0.90068,0.80453,0.91917,0.67357,0.80102,0.91849,0.91801,0.71365,0.91622,0.90961,0.78907 +PSM MQEHMR 34 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894828966685704 null null 2 416.18372 416.18364081688 ms_run[1]:index=33 null null null null 0.98712,0.98906,0.99189,0.98772,0.99073,0.98986 +PSM HNSYTAC+57.021ETHK 35 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8552879715959231 null null 2 674.29083 674.29094231688 ms_run[1]:index=34 null null null null 0.91161,0.92276,0.92215,0.75983,0.57698,0.64840,0.90726,0.92049,0.92356,0.92284,0.92449 +PSM WAPGHATPFSDESSSR 36 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43844590730526867 null null 2 867.4 866.3897028168802 ms_run[1]:index=35 null null null 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4.1.1.dev15+gcedfaa7.d20240625] 0.9865922451019287 null null 2 492.77188 492.77164831688003 ms_run[1]:index=42 null null null null 0.98637,0.98900,0.98957,0.98818,0.98921,0.98818,0.98726,0.97004,0.98958 +PSM TKYTSSK 44 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.977924220263958 null null 2 407.71896 407.71888431688 ms_run[1]:index=43 null null null null 0.98495,0.98298,0.98361,0.98325,0.98555,0.93525,0.98402 +PSM SSFSQHAR 45 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9911030067337884 null null 2 460.22247 460.22266531687995 ms_run[1]:index=44 null null null null 0.99131,0.99140,0.99089,0.99075,0.99078,0.99212,0.99089,0.99124 +PSM SYTSSDTAHK 46 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8599473617293618 null null 2 548.73834 548.7489013168799 ms_run[1]:index=45 null null null null 0.92316,0.92249,0.69404,0.88593,0.67066,0.74161,0.92698,0.92628,0.91877,0.92507 +PSM GTGHTDAENEEVK 47 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6680682482463973 null null 2 693.80896 693.81021881688 ms_run[1]:index=46 null null null null 0.82323,0.80847,0.54724,0.46113,0.45871,0.66241,0.80819,0.56945,0.81953,0.69455,0.49138,0.58402,0.79585 +PSM NEKSEETTEEEVK 48 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7301746702619961 null null 2 776.3595 776.3546553168801 ms_run[1]:index=47 null null null null 0.85148,0.85378,0.52621,0.52819,0.47325,0.67612,0.85314,0.60486,0.86022,0.85298,0.83021,0.68631,0.76565 +PSM KQEEEPNEDTASTSK 49 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9210587590932846 null null 2 846.8801 846.88156881688 ms_run[1]:index=48 null null null null 0.94103,0.95696,0.85467,0.95359,0.83247,0.95710,0.95140,0.93730,0.90773,0.95238,0.95063,0.87036,0.95098,0.81020,0.95436 +PSM NKPGVYTK 50 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9890277054574754 null null 2 453.75558 453.75580581688007 ms_run[1]:index=49 null null null null 0.98844,0.98980,0.99009,0.98958,0.98979,0.98914,0.98524,0.98951 +PSM RPHETGPK 51 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.2289043515920639 null null 2 458.71735 461.2486793168801 ms_run[1]:index=50 null null null null 0.75371,0.81041,0.48279,0.64929,0.75662,0.86533,0.86147,0.87961 +PSM NHGEEHC+57.021AEHK 52 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6672931350767612 null null 2 674.28986 674.2783748168799 ms_run[1]:index=51 null null null null 0.65896,0.82739,0.45964,0.43152,0.81703,0.59720,0.46490,0.62073,0.82695,0.65546,0.81990 +PSM MLDHEGK 53 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9850692301988602 null null 2 415.19717 415.19727081688006 ms_run[1]:index=52 null null null null 0.98767,0.98965,0.98539,0.98816,0.96602,0.98826,0.98794 +PSM 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0.97224,0.97328,0.97316,0.97085,0.97283,0.78519,0.97378,0.96353,0.97323,0.97306,0.97223,0.97381 +PSM NSYTN+0.984GHSSDK 105 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6759249443809191 null null 2 605.7616 605.75217631688 ms_run[1]:index=104 null null null null 0.80744,0.47209,0.48691,0.43885,0.55379,0.57064,0.61858,0.83322,0.82685,0.83470,0.83499 +PSM APTQGEC+57.021HC+57.021DQTF 106 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6652015820145607 null null 2 775.8415 775.8035578168799 ms_run[1]:index=105 null null null null 0.42189,0.79374,0.76732,0.44555,0.50619,0.52009,0.46332,0.59417,0.82448,0.66210,0.82893,0.82902,0.82790 +PSM NVHELEK 107 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9881609752774239 null null 2 434.7295 434.72979181688004 ms_run[1]:index=106 null null null null 0.98844,0.98742,0.98892,0.98666,0.98955,0.98984,0.98553 +PSM YPNHSVDR 108 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9701713191138374 null null 2 494.2362 494.23577281688 ms_run[1]:index=107 null null null null 0.98136,0.88748,0.97896,0.98037,0.98181,0.97936,0.98056,0.98167 +PSM NKEGEVDYAK 109 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8123747543855147 null null 2 576.78033 576.7802103168799 ms_run[1]:index=108 null null null null 0.90083,0.90001,0.89895,0.59818,0.57671,0.56759,0.90301,0.89488,0.90020,0.89448 +PSM LRPEPNTGK 110 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.052142149209976174 null null 2 499.27567 506.28271881688005 ms_run[1]:index=109 null null null null 0.96482,0.96376,0.96742,0.96250,0.96909,0.84115,0.96040,0.94795,0.93244 +PSM NN+0.984EELNK 111 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20876559987664223 null null 2 421.71188 431.20106381688004 ms_run[1]:index=110 null null null null 0.89154,0.89164,0.89013,0.88795,0.88142,0.61297,0.87860 +PSM PHESNYEEDGK 112 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3362173897524675 null null 2 646.7648 652.77311331688 ms_run[1]:index=111 null null null null 0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 +PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 +PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 +PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 +PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 +PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 +PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 +PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 +PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 +PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 +PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 +PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 +PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 +PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 +PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 +PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 +PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index d93b748c..8a1e46ea 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -127,64 +127,44 @@ def main() -> None: nargs=-1, type=click.Path(exists=True, dir_okay=False), ) +@click.option( + "--evaluate", + "-e", + is_flag=True, + default=False, + help="Run in evaluation mode.", +) def sequence( peak_path: Tuple[str], model: Optional[str], config: Optional[str], output: Optional[str], verbosity: str, + evaluate: bool, ) -> None: """De novo sequence peptides from tandem mass spectra. - PEAK_PATH must be one or more mzMl, mzXML, or MGF files from which + PEAK_PATH must be one or more mzML, mzXML, or MGF files from which to sequence peptides. """ output = setup_logging(output, verbosity) config, model = setup_model(model, config, output, False) start_time = time.time() with ModelRunner(config, model) as runner: - logger.info("Sequencing peptides from:") + logger.info( + "Sequencing %speptides from:", + "and evaluating " if evaluate else "", + ) for peak_file in peak_path: logger.info(" %s", peak_file) - runner.predict(peak_path, output) + runner.predict(peak_path, output, evaluate=evaluate) psms = runner.writer.psms utils.log_sequencing_report( psms, start_time=start_time, end_time=time.time() ) -@main.command(cls=_SharedParams) -@click.argument( - "annotated_peak_path", - required=True, - nargs=-1, - type=click.Path(exists=True, dir_okay=False), -) -def evaluate( - annotated_peak_path: Tuple[str], - model: Optional[str], - config: Optional[str], - output: Optional[str], - verbosity: str, -) -> None: - """Evaluate de novo peptide sequencing performance. - - ANNOTATED_PEAK_PATH must be one or more annoated MGF files, - such as those provided by MassIVE-KB. - """ - output = setup_logging(output, verbosity) - config, model = setup_model(model, config, output, False) - start_time = time.time() - with ModelRunner(config, model) as runner: - logger.info("Sequencing and evaluating peptides from:") - for peak_file in annotated_peak_path: - logger.info(" %s", peak_file) - - runner.evaluate(annotated_peak_path) - utils.log_run_report(start_time=start_time, end_time=time.time()) - - @main.command(cls=_SharedParams) @click.argument( "train_peak_path", diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 0914db20..2546a2be 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -116,36 +116,9 @@ def train( self.loaders.val_dataloader(), ) - def evaluate(self, peak_path: Iterable[str]) -> None: - """Evaluate peptide sequence preditions from a trained Casanovo model. - - Parameters - ---------- - peak_path : iterable of str - The path with MS data files for predicting peptide sequences. - - Returns - ------- - self - """ - self.writer = ms_io.MztabWriter(Path("foo.mztab")) - self.writer.set_metadata( - self.config, - model=str(self.model_filename), - config_filename=self.config.file, - ) - - self.initialize_trainer(train=False) - self.initialize_model(train=False) - self.model.out_writer = self.writer - - test_index = self._get_index(peak_path, True, "evaluation") - self.writer.set_ms_run(test_index.ms_files) - self.initialize_data_module(test_index=test_index) - self.loaders.setup(stage="test", annotated=True) - self.trainer.validate(self.model, self.loaders.test_dataloader()) - - def predict(self, peak_path: Iterable[str], output: str) -> None: + def predict( + self, peak_path: Iterable[str], output: str, evaluate=False + ) -> None: """Predict peptide sequences with a trained Casanovo model. Parameters @@ -154,6 +127,10 @@ def predict(self, peak_path: Iterable[str], output: str) -> None: The path with the MS data files for predicting peptide sequences. output : str Where should the output be saved? + evaluate: str + whether to run model evaluation in addition to inference + Note: peak_path most point to annotated MS data files when + running model evaluation Returns ------- @@ -170,11 +147,17 @@ def predict(self, peak_path: Iterable[str], output: str) -> None: self.initialize_model(train=False) self.model.out_writer = self.writer - test_index = self._get_index(peak_path, False, "") + test_index = self._get_index( + peak_path, evaluate, "evaluation" if evaluate else "" + ) self.writer.set_ms_run(test_index.ms_files) self.initialize_data_module(test_index=test_index) - self.loaders.setup(stage="test", annotated=False) - self.trainer.predict(self.model, self.loaders.test_dataloader()) + self.loaders.setup(stage="test", annotated=evaluate) + + if evaluate: + self.trainer.validate(self.model, self.loaders.test_dataloader()) + else: + self.trainer.predict(self.model, self.loaders.test_dataloader()) def initialize_trainer(self, train: bool) -> None: """Initialize the lightning Trainer. diff --git a/foo2.mztab b/foo2.mztab new file mode 100644 index 00000000..c95f7791 --- /dev/null +++ b/foo2.mztab @@ -0,0 +1,189 @@ +MTD mzTab-version 1.0.0 +MTD mzTab-mode Summary +MTD mzTab-type Identification +MTD description Casanovo identification file foo2 +MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] +MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] +MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] +MTD fixed_mod[1]-site C +MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[1]-site N +MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[2]-site Q +MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] +MTD variable_mod[3]-site M +MTD variable_mod[4] [UNIMOD, UNIMOD:385, Ammonia-loss, ] +MTD variable_mod[4]-site N-term +MTD variable_mod[5] [UNIMOD, UNIMOD:1, Acetyl, ] +MTD variable_mod[5]-site N-term +MTD variable_mod[6] [UNIMOD, UNIMOD:5, Carbamyl, ] +MTD variable_mod[6]-site N-term +MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt +MTD software[1]-setting[2] config_filename = default +MTD software[1]-setting[3] precursor_mass_tol = 50.0 +MTD software[1]-setting[4] isotope_error_range = (0, 1) +MTD software[1]-setting[5] min_peptide_len = 6 +MTD software[1]-setting[6] predict_batch_size = 1024 +MTD software[1]-setting[7] n_beams = 1 +MTD software[1]-setting[8] top_match = 1 +MTD software[1]-setting[9] accelerator = auto +MTD software[1]-setting[10] devices = None +MTD software[1]-setting[11] random_seed = 454 +MTD software[1]-setting[12] n_log = 1 +MTD software[1]-setting[13] tb_summarywriter = None +MTD software[1]-setting[14] save_top_k = 5 +MTD software[1]-setting[15] model_save_folder_path = +MTD software[1]-setting[16] val_check_interval = 50000 +MTD software[1]-setting[17] n_peaks = 150 +MTD software[1]-setting[18] min_mz = 50.0 +MTD software[1]-setting[19] max_mz = 2500.0 +MTD software[1]-setting[20] min_intensity = 0.01 +MTD software[1]-setting[21] remove_precursor_tol = 2.0 +MTD software[1]-setting[22] max_charge = 10 +MTD software[1]-setting[23] dim_model = 512 +MTD software[1]-setting[24] n_head = 8 +MTD software[1]-setting[25] dim_feedforward = 1024 +MTD software[1]-setting[26] n_layers = 9 +MTD software[1]-setting[27] dropout = 0.0 +MTD software[1]-setting[28] dim_intensity = None +MTD software[1]-setting[29] max_length = 100 +MTD software[1]-setting[30] warmup_iters = 100000 +MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 +MTD software[1]-setting[32] learning_rate = 0.0005 +MTD software[1]-setting[33] weight_decay = 1e-05 +MTD software[1]-setting[34] train_label_smoothing = 0.01 +MTD software[1]-setting[35] train_batch_size = 32 +MTD software[1]-setting[36] max_epochs = 30 +MTD software[1]-setting[37] num_sanity_val_steps = 0 +MTD software[1]-setting[38] calculate_precision = False +MTD software[1]-setting[40] n_workers = 0 +MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf +PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores +PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 +PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 +PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 +PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 +PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 +PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 +PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 +PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 +PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 +PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 +PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 +PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 +PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 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null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879539277818468 null null 2 441.73788 441.73761731688 ms_run[1]:index=27 null null null null 0.98716,0.98573,0.98970,0.98983,0.98921,0.98323,0.98926,0.98847 +PSM LQHEATAATQK 29 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9673882275819778 null null 2 599.3142 599.31474381688 ms_run[1]:index=28 null null null null 0.97810,0.97690,0.97761,0.96875,0.88905,0.98107,0.97901,0.94171,0.98001,0.97853,0.97914 +PSM KEAPAPPK 30 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.99110433128145 null null 2 419.24496 419.24507831688004 ms_run[1]:index=29 null null null null 0.98966,0.99341,0.99059,0.99097,0.99120,0.99191,0.99078,0.99143 +PSM ERDELR 31 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9874146069799151 null null 2 409.2106 409.2117663168801 ms_run[1]:index=30 null null null null 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MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9210587590932846 null null 2 846.8801 846.88156881688 ms_run[1]:index=48 null null null null 0.94103,0.95696,0.85467,0.95359,0.83247,0.95710,0.95140,0.93730,0.90773,0.95238,0.95063,0.87036,0.95098,0.81020,0.95436 +PSM NKPGVYTK 50 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9890277054574754 null null 2 453.75558 453.75580581688007 ms_run[1]:index=49 null null null null 0.98844,0.98980,0.99009,0.98958,0.98979,0.98914,0.98524,0.98951 +PSM RPHETGPK 51 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.2289043515920639 null null 2 458.71735 461.2486793168801 ms_run[1]:index=50 null null null null 0.75371,0.81041,0.48279,0.64929,0.75662,0.86533,0.86147,0.87961 +PSM NHGEEHC+57.021AEHK 52 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6672931350767612 null null 2 674.28986 674.2783748168799 ms_run[1]:index=51 null null null null 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ms_run[1]:index=105 null null null null 0.42189,0.79374,0.76732,0.44555,0.50619,0.52009,0.46332,0.59417,0.82448,0.66210,0.82893,0.82902,0.82790 +PSM NVHELEK 107 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9881609752774239 null null 2 434.7295 434.72979181688004 ms_run[1]:index=106 null null null null 0.98844,0.98742,0.98892,0.98666,0.98955,0.98984,0.98553 +PSM YPNHSVDR 108 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9701713191138374 null null 2 494.2362 494.23577281688 ms_run[1]:index=107 null null null null 0.98136,0.88748,0.97896,0.98037,0.98181,0.97936,0.98056,0.98167 +PSM NKEGEVDYAK 109 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8123747543855147 null null 2 576.78033 576.7802103168799 ms_run[1]:index=108 null null null null 0.90083,0.90001,0.89895,0.59818,0.57671,0.56759,0.90301,0.89488,0.90020,0.89448 +PSM LRPEPNTGK 110 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.052142149209976174 null null 2 499.27567 506.28271881688005 ms_run[1]:index=109 null null null null 0.96482,0.96376,0.96742,0.96250,0.96909,0.84115,0.96040,0.94795,0.93244 +PSM NN+0.984EELNK 111 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20876559987664223 null null 2 421.71188 431.20106381688004 ms_run[1]:index=110 null null null null 0.89154,0.89164,0.89013,0.88795,0.88142,0.61297,0.87860 +PSM PHESNYEEDGK 112 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3362173897524675 null null 2 646.7648 652.77311331688 ms_run[1]:index=111 null null null null 0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 +PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 +PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 +PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 +PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 +PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 +PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 +PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 +PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 +PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 +PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 +PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 +PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 +PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 +PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 +PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 +PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 From c59edce027d99db60a243bbad6e49c0fbd50eb7c Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Wed, 31 Jul 2024 10:46:57 -0700 Subject: [PATCH 03/36] adapted unit test to new model runner and model functionality --- tests/test_integration.py | 48 ++++++++++++++++++++++----------- tests/unit_tests/test_runner.py | 7 ++--- tests/unit_tests/test_unit.py | 5 ++-- 3 files changed, 40 insertions(+), 20 deletions(-) diff --git a/tests/test_integration.py b/tests/test_integration.py index e5d4b285..6b2a0b7b 100644 --- a/tests/test_integration.py +++ b/tests/test_integration.py @@ -35,24 +35,45 @@ def test_train_and_run( assert result.exit_code == 0 assert model_file.exists() - # Try evaluating: - eval_args = [ - "evaluate", + # Try predicting: + output_filename = tmp_path / "test.mztab" + predict_args = [ + "sequence", "--model", str(model_file), "--config", - str(tiny_config), + tiny_config, "--output", - str(tmp_path / "eval"), + str(output_filename), str(mgf_small), + str(mzml_small), ] - result = run(eval_args) + result = run(predict_args) assert result.exit_code == 0 + assert output_filename.is_file() - # Finally try predicting: - output_filename = tmp_path / "test.mztab" - predict_args = [ + mztab = pyteomics.mztab.MzTab(str(output_filename)) + # Verify that both input peak files are listed in the metadata. + for i, filename in enumerate(["small.mgf", "small.mzml"], 1): + assert f"ms_run[{i}]-location" in mztab.metadata + assert mztab.metadata[f"ms_run[{i}]-location"].endswith(filename) + + # Verify that the spectrum predictions are correct + # and indexed according to the peak input file type. + psms = mztab.spectrum_match_table + assert psms.loc[1, "sequence"] == "LESLLEK" + assert psms.loc[1, "spectra_ref"] == "ms_run[1]:index=0" + assert psms.loc[2, "sequence"] == "PEPTLDEK" + assert psms.loc[2, "spectra_ref"] == "ms_run[1]:index=1" + assert psms.loc[3, "sequence"] == "LESLLEK" + assert psms.loc[3, "spectra_ref"] == "ms_run[2]:scan=17" + assert psms.loc[4, "sequence"] == "PEPTLDEK" + assert psms.loc[4, "spectra_ref"] == "ms_run[2]:scan=111" + + # Finally, try evaluating: + output_filename = tmp_path / "test-eval.mztab" + eval_args = [ "sequence", "--model", str(model_file), @@ -62,15 +83,16 @@ def test_train_and_run( str(output_filename), str(mgf_small), str(mzml_small), + "--evaluate", ] - result = run(predict_args) + result = run(eval_args) assert result.exit_code == 0 assert output_filename.is_file() mztab = pyteomics.mztab.MzTab(str(output_filename)) # Verify that both input peak files are listed in the metadata. - for i, filename in enumerate(["small.mgf", "small.mzml"], 1): + for i, filename in enumerate(["small.mgf"], 1): assert f"ms_run[{i}]-location" in mztab.metadata assert mztab.metadata[f"ms_run[{i}]-location"].endswith(filename) @@ -81,10 +103,6 @@ def test_train_and_run( assert psms.loc[1, "spectra_ref"] == "ms_run[1]:index=0" assert psms.loc[2, "sequence"] == "PEPTLDEK" assert psms.loc[2, "spectra_ref"] == "ms_run[1]:index=1" - assert psms.loc[3, "sequence"] == "LESLLEK" - assert psms.loc[3, "spectra_ref"] == "ms_run[2]:scan=17" - assert psms.loc[4, "sequence"] == "PEPTLDEK" - assert psms.loc[4, "spectra_ref"] == "ms_run[2]:scan=111" def test_auxilliary_cli(tmp_path, monkeypatch): diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index 2d0513bd..96a2738a 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -56,6 +56,7 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): config.max_epochs = 1 config.n_layers = 1 ckpt = tmp_path / "test.ckpt" + output_file = tmp_path / "out" with ModelRunner(config=config) as runner: runner.train([mgf_small], [mgf_small]) @@ -83,7 +84,7 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): with torch.device("meta"): with ModelRunner(other_config, model_filename=str(ckpt)) as runner: with pytest.raises(NotImplementedError) as err: - runner.evaluate([mgf_small]) + runner.predict([mgf_small], output_file, evaluate=True) assert "meta tensor; no data!" in str(err.value) @@ -95,11 +96,11 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): # Shouldn't work: with ModelRunner(other_config, model_filename=str(ckpt)) as runner: with pytest.raises(RuntimeError): - runner.evaluate([mgf_small]) + runner.predict([mgf_small], output_file, evaluate=True) # Should work: with ModelRunner(config=config, model_filename=str(ckpt)) as runner: - runner.evaluate([mgf_small]) + runner.predict([mgf_small], output_file, evaluate=True) def test_save_and_load_weights_deprecated(tmp_path, mgf_small, tiny_config): diff --git a/tests/unit_tests/test_unit.py b/tests/unit_tests/test_unit.py index f615a099..2a62000b 100644 --- a/tests/unit_tests/test_unit.py +++ b/tests/unit_tests/test_unit.py @@ -597,10 +597,11 @@ def test_train_val_step_functions(): spectra = torch.zeros(1, 5, 2) precursors = torch.tensor([[469.25364, 2.0, 235.63410]]) peptides = ["PEPK"] - batch = (spectra, precursors, peptides) + spectrum_id = "foobar" + batch = (spectra, precursors, spectrum_id, peptides) train_step_loss = model.training_step(batch) - val_step_loss = model.validation_step(batch) + val_step_loss, _ = model.validation_step(batch) # Check if valid loss value returned assert train_step_loss > 0 From b9f843aa6340a00501ed5b7c260003632303c6b1 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Wed, 31 Jul 2024 11:07:47 -0700 Subject: [PATCH 04/36] updated documentation --- casanovo/data/datasets.py | 7 ++++++- casanovo/denovo/dataloaders.py | 12 ++++++++---- casanovo/denovo/model.py | 4 ++-- casanovo/denovo/model_runner.py | 6 +++++- 4 files changed, 21 insertions(+), 8 deletions(-) diff --git a/casanovo/data/datasets.py b/casanovo/data/datasets.py index f7b2fe7e..bd3d93af 100644 --- a/casanovo/data/datasets.py +++ b/casanovo/data/datasets.py @@ -235,7 +235,9 @@ def __init__( random_state=random_state, ) - def __getitem__(self, idx: int) -> Tuple[torch.Tensor, float, int, str]: + def __getitem__( + self, idx: int + ) -> Tuple[torch.Tensor, float, int, Tuple[str, str], str]: """ Return the annotated MS/MS spectrum with the given index. @@ -252,6 +254,9 @@ def __getitem__(self, idx: int) -> Tuple[torch.Tensor, float, int, str]: The precursor m/z. precursor_charge : int The precursor charge. + spectrum_id: Tuple[str, str] + The unique spectrum identifier, formed by its original peak file and + identifier (index or scan number) therein. annotation : str The peptide annotation of the spectrum. """ diff --git a/casanovo/denovo/dataloaders.py b/casanovo/denovo/dataloaders.py index ba58d83c..9a8b1e32 100644 --- a/casanovo/denovo/dataloaders.py +++ b/casanovo/denovo/dataloaders.py @@ -175,8 +175,8 @@ def predict_dataloader(self) -> torch.utils.data.DataLoader: def prepare_batch( - batch: List[Tuple[torch.Tensor, float, int, str]] -) -> Tuple[torch.Tensor, torch.Tensor, np.ndarray]: + batch: List[Tuple[torch.Tensor, float, int, str, Optional[str]]] +) -> Tuple[torch.Tensor, torch.Tensor, np.ndarray, np.ndarray | None]: """ Collate MS/MS spectra into a batch. @@ -185,10 +185,11 @@ def prepare_batch( Parameters ---------- - batch : List[Tuple[torch.Tensor, float, int, str]] + batch : List[Tuple[torch.Tensor, float, int, str, Optional[str]]] A batch of data from an AnnotatedSpectrumDataset, consisting of for each spectrum (i) a tensor with the m/z and intensity peak values, (ii), the - precursor m/z, (iii) the precursor charge, (iv) the spectrum identifier. + precursor m/z, (iii) the precursor charge, (iv) the spectrum identifier, + (v) optionally the peptide sequence annotation Returns ------- @@ -201,6 +202,9 @@ def prepare_batch( spectrum_ids : np.ndarray The spectrum identifiers (during de novo sequencing) or peptide sequences (during training). + annotations : np.ndarray | None + The peptide annotations of the spectra if provided by the dataset, + None otherwise """ batch_list = list(zip(*batch)) spectra, precursor_mzs, precursor_charges, spectrum_ids = batch_list[0:4] diff --git a/casanovo/denovo/model.py b/casanovo/denovo/model.py index 29acaf40..aae8d925 100644 --- a/casanovo/denovo/model.py +++ b/casanovo/denovo/model.py @@ -773,7 +773,7 @@ def validation_step( ---------- batch : Tuple[torch.Tensor, torch.Tensor, List[str]] A batch of (i) MS/MS spectra, (ii) precursor information, (iii) - peptide sequences. + spectrum identifiers, (iv) peptide sequence annotations Returns ------- @@ -788,7 +788,7 @@ def validation_step( # Calculate and log amino acid and peptide match evaluation metrics from # the predicted peptides. - peptides_pred, peptides_true = [], batch[2] + peptides_pred, peptides_true = [], batch[3] for spectrum_preds in forward_step: for _, _, pred in spectrum_preds: peptides_pred.append(pred) diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 2546a2be..f5990097 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -121,6 +121,9 @@ def predict( ) -> None: """Predict peptide sequences with a trained Casanovo model. + Can also evaluate model during prediction if provided with annotated + peak files. + Parameters ---------- peak_path : iterable of str @@ -130,7 +133,8 @@ def predict( evaluate: str whether to run model evaluation in addition to inference Note: peak_path most point to annotated MS data files when - running model evaluation + running model evaluation. Files that are not an annotated + peak file format will be ignored if evaluate is set to true. Returns ------- From 6716db6cbcc8e272737bca05ea2216fedeee1bd3 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Wed, 31 Jul 2024 11:20:53 -0700 Subject: [PATCH 05/36] removed log and result files --- bar.mztab | 189 ----------------------------------------------------- bar2.mztab | 189 ----------------------------------------------------- foo.mztab | 189 ----------------------------------------------------- foo2.mztab | 189 ----------------------------------------------------- 4 files changed, 756 deletions(-) delete mode 100644 bar.mztab delete mode 100644 bar2.mztab delete mode 100644 foo.mztab delete mode 100644 foo2.mztab diff --git a/bar.mztab b/bar.mztab deleted file mode 100644 index cbcd1bb5..00000000 --- a/bar.mztab +++ /dev/null @@ -1,189 +0,0 @@ -MTD mzTab-version 1.0.0 -MTD mzTab-mode Summary -MTD mzTab-type Identification -MTD description Casanovo identification file bar -MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] -MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] -MTD fixed_mod[1]-site C -MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[1]-site N -MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[2]-site Q -MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] -MTD variable_mod[3]-site M -MTD variable_mod[4] [UNIMOD, UNIMOD:5, Carbamyl, ] -MTD variable_mod[4]-site N-term -MTD variable_mod[5] [UNIMOD, UNIMOD:385, Ammonia-loss, ] -MTD variable_mod[5]-site N-term -MTD variable_mod[6] [UNIMOD, UNIMOD:1, Acetyl, ] -MTD variable_mod[6]-site N-term -MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt -MTD software[1]-setting[2] config_filename = default -MTD software[1]-setting[3] precursor_mass_tol = 50.0 -MTD software[1]-setting[4] isotope_error_range = (0, 1) -MTD software[1]-setting[5] min_peptide_len = 6 -MTD software[1]-setting[6] predict_batch_size = 1024 -MTD software[1]-setting[7] n_beams = 1 -MTD software[1]-setting[8] top_match = 1 -MTD software[1]-setting[9] accelerator = auto -MTD software[1]-setting[10] devices = None -MTD software[1]-setting[11] random_seed = 454 -MTD software[1]-setting[12] n_log = 1 -MTD software[1]-setting[13] tb_summarywriter = None -MTD software[1]-setting[14] save_top_k = 5 -MTD software[1]-setting[15] model_save_folder_path = -MTD software[1]-setting[16] val_check_interval = 50000 -MTD software[1]-setting[17] n_peaks = 150 -MTD software[1]-setting[18] min_mz = 50.0 -MTD software[1]-setting[19] max_mz = 2500.0 -MTD software[1]-setting[20] min_intensity = 0.01 -MTD software[1]-setting[21] remove_precursor_tol = 2.0 -MTD software[1]-setting[22] max_charge = 10 -MTD software[1]-setting[23] dim_model = 512 -MTD software[1]-setting[24] n_head = 8 -MTD software[1]-setting[25] dim_feedforward = 1024 -MTD software[1]-setting[26] n_layers = 9 -MTD software[1]-setting[27] dropout = 0.0 -MTD software[1]-setting[28] dim_intensity = None -MTD software[1]-setting[29] max_length = 100 -MTD software[1]-setting[30] warmup_iters = 100000 -MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 -MTD software[1]-setting[32] learning_rate = 0.0005 -MTD software[1]-setting[33] weight_decay = 1e-05 -MTD software[1]-setting[34] train_label_smoothing = 0.01 -MTD software[1]-setting[35] train_batch_size = 32 -MTD software[1]-setting[36] max_epochs = 30 -MTD software[1]-setting[37] num_sanity_val_steps = 0 -MTD software[1]-setting[38] calculate_precision = False -MTD software[1]-setting[40] n_workers = 0 -MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf -PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores -PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 -PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 -PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 -PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 -PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 -PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 -PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 -PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 -PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 -PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 -PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 -PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 -PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 -PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 -PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 -PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9672952890396118 null null 2 614.33795 614.33821831688 ms_run[1]:index=15 null null null null 0.97399,0.97959,0.97837,0.97845,0.96474,0.84979,0.97928,0.97613,0.97886,0.97760,0.97960,0.97994 -PSM LQEEERER 17 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.975036793284946 null null 2 544.77 544.77017681688 ms_run[1]:index=16 null null null null 0.91222,0.98079,0.98579,0.98252,0.98429,0.98225,0.98285,0.98220 -PSM TRGHESEMK 18 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1844959855079651 null null 2 539.25323 537.75346831688 ms_run[1]:index=17 null null null null 0.90297,0.90465,0.82135,0.90041,0.64139,0.62194,0.66087,0.89718,0.90124 -PSM +42.011KVEDPPRK 19 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.24581749439239498 null null 2 507.26154 505.78509881688007 ms_run[1]:index=18 null null null null 0.77158,0.66196,0.86775,0.87090,0.70578,0.61787,0.85217,0.69678,0.62489 -PSM TESPAEGKQEEEK 20 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.868788189121655 null null 2 731.3395 731.3388133168802 ms_run[1]:index=19 null null null null 0.92347,0.91621,0.74657,0.61987,0.87546,0.65200,0.92947,0.92629,0.93151,0.92995,0.92921,0.92534,0.92826 -PSM LVEEETKK 21 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879584113756815 null null 2 488.27112 488.27148531688005 ms_run[1]:index=20 null null null null 0.98623,0.98691,0.98852,0.98742,0.98734,0.98694,0.99077,0.98849 -PSM KAETLGEK 22 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9864536391364204 null null 2 438.24524 438.24527081688 ms_run[1]:index=21 null null null null 0.98740,0.98704,0.98770,0.98844,0.98931,0.98661,0.98774,0.97524 -PSM C+57.021LKPNETK 23 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9895809359020658 null null 2 495.25775 495.25785531688 ms_run[1]:index=22 null null null null 0.98927,0.98929,0.98595,0.99043,0.99001,0.99081,0.98784,0.99231 -PSM GHQALER 24 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9861482679843903 null null 2 405.71454 405.71447681688 ms_run[1]:index=23 null null null null 0.98369,0.97763,0.98807,0.98786,0.98838,0.98693,0.98818 -PSM TNNLRPK 25 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9859854802489281 null null 2 421.74548 421.74577181688005 ms_run[1]:index=24 null null null null 0.98893,0.99008,0.98974,0.98259,0.98795,0.97375,0.98633 -PSM +43.006DTPGHATPGHGAGTQER 26 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.22608531070382976 null null 2 867.40045 866.39330131688 ms_run[1]:index=25 null null null null 0.85561,0.57927,0.49126,0.50495,0.70489,0.76038,0.75372,0.53050,0.87917,0.87740,0.88139,0.87799,0.88406,0.88016,0.88217,0.87672,0.82864,0.77355 -PSM KSYTTPK 27 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8933427818119526 null null 2 412.72778 412.72925231688004 ms_run[1]:index=26 null null null null 0.93932,0.94376,0.93479,0.61684,0.94099,0.93574,0.89386 -PSM VLEGHAEK 28 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879539277818468 null null 2 441.73788 441.73761731688 ms_run[1]:index=27 null null null null 0.98716,0.98573,0.98970,0.98983,0.98921,0.98323,0.98926,0.98847 -PSM LQHEATAATQK 29 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9673882275819778 null null 2 599.3142 599.31474381688 ms_run[1]:index=28 null null null null 0.97810,0.97690,0.97761,0.96875,0.88905,0.98107,0.97901,0.94171,0.98001,0.97853,0.97914 -PSM KEAPAPPK 30 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.99110433128145 null null 2 419.24496 419.24507831688004 ms_run[1]:index=29 null null null null 0.98966,0.99341,0.99059,0.99097,0.99120,0.99191,0.99078,0.99143 -PSM ERDELR 31 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9874146069799151 null null 2 409.2106 409.2117663168801 ms_run[1]:index=30 null null null null 0.98921,0.98706,0.98802,0.98241,0.98891,0.98739 -PSM EVLHANNR 32 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8818797965844473 null null 2 476.75156 476.75158981687997 ms_run[1]:index=31 null null null null 0.93772,0.73514,0.67541,0.93265,0.93705,0.93603,0.93502,0.91176 -PSM NNTLTPNKPNK 33 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1514618446429571 null null 2 613.8276 620.83584181688 ms_run[1]:index=32 null null null null 0.90068,0.80453,0.91917,0.67357,0.80102,0.91849,0.91801,0.71365,0.91622,0.90961,0.78907 -PSM MQEHMR 34 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894828966685704 null null 2 416.18372 416.18364081688 ms_run[1]:index=33 null null null null 0.98712,0.98906,0.99189,0.98772,0.99073,0.98986 -PSM HNSYTAC+57.021ETHK 35 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8552879715959231 null null 2 674.29083 674.29094231688 ms_run[1]:index=34 null null null null 0.91161,0.92276,0.92215,0.75983,0.57698,0.64840,0.90726,0.92049,0.92356,0.92284,0.92449 -PSM WAPGHATPFSDESSSR 36 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43844590730526867 null null 2 867.4 866.3897028168802 ms_run[1]:index=35 null null null null 0.62368,0.35030,0.34498,0.43399,0.63293,0.39463,0.54277,0.45963,0.77829,0.76285,0.61244,0.56565,0.66891,0.77050,0.38220,0.45175 -PSM GDDETLHK 37 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9814771148893568 null null 2 457.71384 457.71433481688 ms_run[1]:index=36 null null null null 0.98366,0.98677,0.98606,0.98567,0.97685,0.97706,0.96534,0.98540 -PSM NEKSEEEQSSASVK 38 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9875149647394816 null null 2 776.35913 776.3602803168801 ms_run[1]:index=37 null null null null 0.98915,0.98944,0.98834,0.98835,0.98850,0.98888,0.97847,0.98778,0.98852,0.98666,0.98830,0.98710,0.98650,0.98822 -PSM NNTVTPGGKPGGK 39 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.946726496730532 null null 2 613.82745 613.8280178168801 ms_run[1]:index=38 null null null null 0.93242,0.80678,0.95406,0.96786,0.88768,0.96598,0.96954,0.96820,0.96772,0.96757,0.96759,0.96293,0.96766 -PSM HNGEEEEETHK 40 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.4023066883285841 null null 2 674.2913 669.7814653168799 ms_run[1]:index=39 null null null null 0.79198,0.79514,0.76636,0.39427,0.42610,0.40046,0.40083,0.39425,0.44152,0.77926,0.78835 -PSM HDSVEER 41 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9554774761199951 null null 2 436.19864 436.1988558168801 ms_run[1]:index=40 null null null null 0.94772,0.95530,0.92708,0.94280,0.96933,0.95420,0.97425 -PSM EGGQVASMEEEK 42 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.48210483216322386 null null 2 648.29266 647.28499981688 ms_run[1]:index=41 null null null null 0.39005,0.43086,0.42453,0.34300,0.64313,0.48547,0.75237,0.73883,0.36843,0.39590,0.47632,0.52967 -PSM AVTKYTSSK 43 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865922451019287 null null 2 492.77188 492.77164831688003 ms_run[1]:index=42 null null null null 0.98637,0.98900,0.98957,0.98818,0.98921,0.98818,0.98726,0.97004,0.98958 -PSM TKYTSSK 44 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.977924220263958 null null 2 407.71896 407.71888431688 ms_run[1]:index=43 null null null null 0.98495,0.98298,0.98361,0.98325,0.98555,0.93525,0.98402 -PSM SSFSQHAR 45 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9911030067337884 null null 2 460.22247 460.22266531687995 ms_run[1]:index=44 null null null null 0.99131,0.99140,0.99089,0.99075,0.99078,0.99212,0.99089,0.99124 -PSM SYTSSDTAHK 46 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8599473617293618 null null 2 548.73834 548.7489013168799 ms_run[1]:index=45 null null null null 0.92316,0.92249,0.69404,0.88593,0.67066,0.74161,0.92698,0.92628,0.91877,0.92507 -PSM GTGHTDAENEEVK 47 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6680682482463973 null null 2 693.80896 693.81021881688 ms_run[1]:index=46 null null null null 0.82323,0.80847,0.54724,0.46113,0.45871,0.66241,0.80819,0.56945,0.81953,0.69455,0.49138,0.58402,0.79585 -PSM NEKSEETTEEEVK 48 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7301746702619961 null null 2 776.3595 776.3546553168801 ms_run[1]:index=47 null null null null 0.85148,0.85378,0.52621,0.52819,0.47325,0.67612,0.85314,0.60486,0.86022,0.85298,0.83021,0.68631,0.76565 -PSM KQEEEPNEDTASTSK 49 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9210587590932846 null null 2 846.8801 846.88156881688 ms_run[1]:index=48 null null null null 0.94103,0.95696,0.85467,0.95359,0.83247,0.95710,0.95140,0.93730,0.90773,0.95238,0.95063,0.87036,0.95098,0.81020,0.95436 -PSM NKPGVYTK 50 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9890277054574754 null null 2 453.75558 453.75580581688007 ms_run[1]:index=49 null null null null 0.98844,0.98980,0.99009,0.98958,0.98979,0.98914,0.98524,0.98951 -PSM RPHETGPK 51 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.2289043515920639 null null 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MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9784338027238846 null null 2 431.2012 431.20106381688004 ms_run[1]:index=101 null null null null 0.98508,0.98284,0.98438,0.97530,0.97293,0.96303,0.97950 -PSM GGSLPQNHLHGH 103 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7780202948130094 null null 2 627.3102 627.3103353168799 ms_run[1]:index=102 null null null null 0.88073,0.88552,0.88639,0.53989,0.48982,0.59155,0.75677,0.88470,0.79813,0.81800,0.81249,0.88578 -PSM EESGKPQHVTVK 104 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9577845564255347 null null 2 669.8538 669.85423681688 ms_run[1]:index=103 null null null null 0.97224,0.97328,0.97316,0.97085,0.97283,0.78519,0.97378,0.96353,0.97323,0.97306,0.97223,0.97381 -PSM NSYTN+0.984GHSSDK 105 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6759249443809191 null null 2 605.7616 605.75217631688 ms_run[1]:index=104 null null null null 0.80744,0.47209,0.48691,0.43885,0.55379,0.57064,0.61858,0.83322,0.82685,0.83470,0.83499 -PSM APTQGEC+57.021HC+57.021DQTF 106 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6652015820145607 null null 2 775.8415 775.8035578168799 ms_run[1]:index=105 null null null null 0.42189,0.79374,0.76732,0.44555,0.50619,0.52009,0.46332,0.59417,0.82448,0.66210,0.82893,0.82902,0.82790 -PSM NVHELEK 107 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9881609752774239 null null 2 434.7295 434.72979181688004 ms_run[1]:index=106 null null null null 0.98844,0.98742,0.98892,0.98666,0.98955,0.98984,0.98553 -PSM YPNHSVDR 108 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9701713191138374 null null 2 494.2362 494.23577281688 ms_run[1]:index=107 null null null null 0.98136,0.88748,0.97896,0.98037,0.98181,0.97936,0.98056,0.98167 -PSM NKEGEVDYAK 109 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8123747543855147 null null 2 576.78033 576.7802103168799 ms_run[1]:index=108 null null null null 0.90083,0.90001,0.89895,0.59818,0.57671,0.56759,0.90301,0.89488,0.90020,0.89448 -PSM LRPEPNTGK 110 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.052142149209976174 null null 2 499.27567 506.28271881688005 ms_run[1]:index=109 null null null null 0.96482,0.96376,0.96742,0.96250,0.96909,0.84115,0.96040,0.94795,0.93244 -PSM NN+0.984EELNK 111 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20876559987664223 null null 2 421.71188 431.20106381688004 ms_run[1]:index=110 null null null null 0.89154,0.89164,0.89013,0.88795,0.88142,0.61297,0.87860 -PSM PHESNYEEDGK 112 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3362173897524675 null null 2 646.7648 652.77311331688 ms_run[1]:index=111 null null null null 0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 -PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 -PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 -PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 -PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 -PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 -PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 -PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 -PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 -PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 -PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 -PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 -PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 -PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 -PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 -PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 -PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 diff --git a/bar2.mztab b/bar2.mztab deleted file mode 100644 index 78f5939c..00000000 --- a/bar2.mztab +++ /dev/null @@ -1,189 +0,0 @@ -MTD mzTab-version 1.0.0 -MTD mzTab-mode Summary -MTD mzTab-type Identification -MTD description Casanovo identification file bar2 -MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] -MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] -MTD fixed_mod[1]-site C -MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[1]-site N -MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[2]-site Q -MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] -MTD variable_mod[3]-site M -MTD variable_mod[4] [UNIMOD, UNIMOD:385, Ammonia-loss, ] -MTD variable_mod[4]-site N-term -MTD variable_mod[5] [UNIMOD, UNIMOD:5, Carbamyl, ] -MTD variable_mod[5]-site N-term -MTD variable_mod[6] [UNIMOD, UNIMOD:1, Acetyl, ] -MTD variable_mod[6]-site N-term -MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt -MTD software[1]-setting[2] config_filename = default -MTD software[1]-setting[3] precursor_mass_tol = 50.0 -MTD software[1]-setting[4] isotope_error_range = (0, 1) -MTD software[1]-setting[5] min_peptide_len = 6 -MTD software[1]-setting[6] predict_batch_size = 1024 -MTD software[1]-setting[7] n_beams = 1 -MTD software[1]-setting[8] top_match = 1 -MTD software[1]-setting[9] accelerator = auto -MTD software[1]-setting[10] devices = None -MTD software[1]-setting[11] random_seed = 454 -MTD software[1]-setting[12] n_log = 1 -MTD software[1]-setting[13] tb_summarywriter = None -MTD software[1]-setting[14] save_top_k = 5 -MTD software[1]-setting[15] model_save_folder_path = -MTD software[1]-setting[16] val_check_interval = 50000 -MTD software[1]-setting[17] n_peaks = 150 -MTD software[1]-setting[18] min_mz = 50.0 -MTD software[1]-setting[19] max_mz = 2500.0 -MTD software[1]-setting[20] min_intensity = 0.01 -MTD software[1]-setting[21] remove_precursor_tol = 2.0 -MTD software[1]-setting[22] max_charge = 10 -MTD software[1]-setting[23] dim_model = 512 -MTD software[1]-setting[24] n_head = 8 -MTD software[1]-setting[25] dim_feedforward = 1024 -MTD software[1]-setting[26] n_layers = 9 -MTD software[1]-setting[27] dropout = 0.0 -MTD software[1]-setting[28] dim_intensity = None -MTD software[1]-setting[29] max_length = 100 -MTD software[1]-setting[30] warmup_iters = 100000 -MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 -MTD software[1]-setting[32] learning_rate = 0.0005 -MTD software[1]-setting[33] weight_decay = 1e-05 -MTD software[1]-setting[34] train_label_smoothing = 0.01 -MTD software[1]-setting[35] train_batch_size = 32 -MTD software[1]-setting[36] max_epochs = 30 -MTD software[1]-setting[37] num_sanity_val_steps = 0 -MTD software[1]-setting[38] calculate_precision = False -MTD software[1]-setting[40] n_workers = 0 -MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf -PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores -PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 -PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 -PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 -PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 -PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 -PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 -PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 -PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 -PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 -PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 -PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 -PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 -PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 -PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 -PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 -PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9672952890396118 null null 2 614.33795 614.33821831688 ms_run[1]:index=15 null null null null 0.97399,0.97959,0.97837,0.97845,0.96474,0.84979,0.97928,0.97613,0.97886,0.97760,0.97960,0.97994 -PSM LQEEERER 17 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.975036793284946 null null 2 544.77 544.77017681688 ms_run[1]:index=16 null null null null 0.91222,0.98079,0.98579,0.98252,0.98429,0.98225,0.98285,0.98220 -PSM TRGHESEMK 18 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1844959855079651 null null 2 539.25323 537.75346831688 ms_run[1]:index=17 null null null null 0.90297,0.90465,0.82135,0.90041,0.64139,0.62194,0.66087,0.89718,0.90124 -PSM +42.011KVEDPPRK 19 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.24581749439239498 null null 2 507.26154 505.78509881688007 ms_run[1]:index=18 null null null null 0.77158,0.66196,0.86775,0.87090,0.70578,0.61787,0.85217,0.69678,0.62489 -PSM TESPAEGKQEEEK 20 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.868788189121655 null null 2 731.3395 731.3388133168802 ms_run[1]:index=19 null null null null 0.92347,0.91621,0.74657,0.61987,0.87546,0.65200,0.92947,0.92629,0.93151,0.92995,0.92921,0.92534,0.92826 -PSM LVEEETKK 21 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879584113756815 null null 2 488.27112 488.27148531688005 ms_run[1]:index=20 null null null null 0.98623,0.98691,0.98852,0.98742,0.98734,0.98694,0.99077,0.98849 -PSM KAETLGEK 22 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9864536391364204 null null 2 438.24524 438.24527081688 ms_run[1]:index=21 null null null null 0.98740,0.98704,0.98770,0.98844,0.98931,0.98661,0.98774,0.97524 -PSM C+57.021LKPNETK 23 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 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MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 -PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 -PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 -PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 -PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 -PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 -PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 -PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 -PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 diff --git a/foo.mztab b/foo.mztab deleted file mode 100644 index aa8a6922..00000000 --- a/foo.mztab +++ /dev/null @@ -1,189 +0,0 @@ -MTD mzTab-version 1.0.0 -MTD mzTab-mode Summary -MTD mzTab-type Identification -MTD description Casanovo identification file foo -MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] -MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] -MTD fixed_mod[1]-site C -MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[1]-site N -MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[2]-site Q -MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] -MTD variable_mod[3]-site M -MTD variable_mod[4] [UNIMOD, UNIMOD:5, Carbamyl, ] -MTD variable_mod[4]-site N-term -MTD variable_mod[5] [UNIMOD, UNIMOD:1, Acetyl, ] -MTD variable_mod[5]-site N-term -MTD variable_mod[6] [UNIMOD, UNIMOD:385, Ammonia-loss, ] -MTD variable_mod[6]-site N-term -MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt -MTD software[1]-setting[2] config_filename = default -MTD software[1]-setting[3] precursor_mass_tol = 50.0 -MTD software[1]-setting[4] isotope_error_range = (0, 1) -MTD software[1]-setting[5] min_peptide_len = 6 -MTD software[1]-setting[6] predict_batch_size = 1024 -MTD software[1]-setting[7] n_beams = 1 -MTD software[1]-setting[8] top_match = 1 -MTD software[1]-setting[9] accelerator = auto -MTD software[1]-setting[10] devices = None -MTD software[1]-setting[11] random_seed = 454 -MTD software[1]-setting[12] n_log = 1 -MTD software[1]-setting[13] tb_summarywriter = None -MTD software[1]-setting[14] save_top_k = 5 -MTD software[1]-setting[15] model_save_folder_path = -MTD software[1]-setting[16] val_check_interval = 50000 -MTD software[1]-setting[17] n_peaks = 150 -MTD software[1]-setting[18] min_mz = 50.0 -MTD software[1]-setting[19] max_mz = 2500.0 -MTD software[1]-setting[20] min_intensity = 0.01 -MTD software[1]-setting[21] remove_precursor_tol = 2.0 -MTD software[1]-setting[22] max_charge = 10 -MTD software[1]-setting[23] dim_model = 512 -MTD software[1]-setting[24] n_head = 8 -MTD software[1]-setting[25] dim_feedforward = 1024 -MTD software[1]-setting[26] n_layers = 9 -MTD software[1]-setting[27] dropout = 0.0 -MTD software[1]-setting[28] dim_intensity = None -MTD software[1]-setting[29] max_length = 100 -MTD software[1]-setting[30] warmup_iters = 100000 -MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 -MTD software[1]-setting[32] learning_rate = 0.0005 -MTD software[1]-setting[33] weight_decay = 1e-05 -MTD software[1]-setting[34] train_label_smoothing = 0.01 -MTD software[1]-setting[35] train_batch_size = 32 -MTD software[1]-setting[36] max_epochs = 30 -MTD software[1]-setting[37] num_sanity_val_steps = 0 -MTD software[1]-setting[38] calculate_precision = False -MTD software[1]-setting[40] n_workers = 0 -MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf -PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores -PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 -PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 -PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 -PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 -PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 -PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 -PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 -PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 -PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 -PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 -PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 -PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 -PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 -PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 -PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 -PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9672952890396118 null null 2 614.33795 614.33821831688 ms_run[1]:index=15 null null null null 0.97399,0.97959,0.97837,0.97845,0.96474,0.84979,0.97928,0.97613,0.97886,0.97760,0.97960,0.97994 -PSM LQEEERER 17 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.975036793284946 null null 2 544.77 544.77017681688 ms_run[1]:index=16 null null null null 0.91222,0.98079,0.98579,0.98252,0.98429,0.98225,0.98285,0.98220 -PSM TRGHESEMK 18 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1844959855079651 null null 2 539.25323 537.75346831688 ms_run[1]:index=17 null null null null 0.90297,0.90465,0.82135,0.90041,0.64139,0.62194,0.66087,0.89718,0.90124 -PSM +42.011KVEDPPRK 19 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.24581749439239498 null null 2 507.26154 505.78509881688007 ms_run[1]:index=18 null null null null 0.77158,0.66196,0.86775,0.87090,0.70578,0.61787,0.85217,0.69678,0.62489 -PSM TESPAEGKQEEEK 20 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.868788189121655 null null 2 731.3395 731.3388133168802 ms_run[1]:index=19 null null null null 0.92347,0.91621,0.74657,0.61987,0.87546,0.65200,0.92947,0.92629,0.93151,0.92995,0.92921,0.92534,0.92826 -PSM LVEEETKK 21 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879584113756815 null null 2 488.27112 488.27148531688005 ms_run[1]:index=20 null null null null 0.98623,0.98691,0.98852,0.98742,0.98734,0.98694,0.99077,0.98849 -PSM KAETLGEK 22 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9864536391364204 null null 2 438.24524 438.24527081688 ms_run[1]:index=21 null null null null 0.98740,0.98704,0.98770,0.98844,0.98931,0.98661,0.98774,0.97524 -PSM C+57.021LKPNETK 23 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9895809359020658 null null 2 495.25775 495.25785531688 ms_run[1]:index=22 null null null null 0.98927,0.98929,0.98595,0.99043,0.99001,0.99081,0.98784,0.99231 -PSM GHQALER 24 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9861482679843903 null null 2 405.71454 405.71447681688 ms_run[1]:index=23 null null null null 0.98369,0.97763,0.98807,0.98786,0.98838,0.98693,0.98818 -PSM TNNLRPK 25 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9859854802489281 null null 2 421.74548 421.74577181688005 ms_run[1]:index=24 null null null null 0.98893,0.99008,0.98974,0.98259,0.98795,0.97375,0.98633 -PSM +43.006DTPGHATPGHGAGTQER 26 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.22608531070382976 null null 2 867.40045 866.39330131688 ms_run[1]:index=25 null null null null 0.85561,0.57927,0.49126,0.50495,0.70489,0.76038,0.75372,0.53050,0.87917,0.87740,0.88139,0.87799,0.88406,0.88016,0.88217,0.87672,0.82864,0.77355 -PSM KSYTTPK 27 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8933427818119526 null null 2 412.72778 412.72925231688004 ms_run[1]:index=26 null null null null 0.93932,0.94376,0.93479,0.61684,0.94099,0.93574,0.89386 -PSM VLEGHAEK 28 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879539277818468 null null 2 441.73788 441.73761731688 ms_run[1]:index=27 null null null null 0.98716,0.98573,0.98970,0.98983,0.98921,0.98323,0.98926,0.98847 -PSM LQHEATAATQK 29 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9673882275819778 null null 2 599.3142 599.31474381688 ms_run[1]:index=28 null null null null 0.97810,0.97690,0.97761,0.96875,0.88905,0.98107,0.97901,0.94171,0.98001,0.97853,0.97914 -PSM KEAPAPPK 30 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.99110433128145 null null 2 419.24496 419.24507831688004 ms_run[1]:index=29 null null null null 0.98966,0.99341,0.99059,0.99097,0.99120,0.99191,0.99078,0.99143 -PSM ERDELR 31 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9874146069799151 null null 2 409.2106 409.2117663168801 ms_run[1]:index=30 null null null null 0.98921,0.98706,0.98802,0.98241,0.98891,0.98739 -PSM EVLHANNR 32 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8818797965844473 null null 2 476.75156 476.75158981687997 ms_run[1]:index=31 null null null null 0.93772,0.73514,0.67541,0.93265,0.93705,0.93603,0.93502,0.91176 -PSM NNTLTPNKPNK 33 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1514618446429571 null null 2 613.8276 620.83584181688 ms_run[1]:index=32 null null null null 0.90068,0.80453,0.91917,0.67357,0.80102,0.91849,0.91801,0.71365,0.91622,0.90961,0.78907 -PSM MQEHMR 34 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894828966685704 null null 2 416.18372 416.18364081688 ms_run[1]:index=33 null null null null 0.98712,0.98906,0.99189,0.98772,0.99073,0.98986 -PSM HNSYTAC+57.021ETHK 35 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8552879715959231 null null 2 674.29083 674.29094231688 ms_run[1]:index=34 null null null null 0.91161,0.92276,0.92215,0.75983,0.57698,0.64840,0.90726,0.92049,0.92356,0.92284,0.92449 -PSM WAPGHATPFSDESSSR 36 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43844590730526867 null null 2 867.4 866.3897028168802 ms_run[1]:index=35 null null null null 0.62368,0.35030,0.34498,0.43399,0.63293,0.39463,0.54277,0.45963,0.77829,0.76285,0.61244,0.56565,0.66891,0.77050,0.38220,0.45175 -PSM GDDETLHK 37 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9814771148893568 null null 2 457.71384 457.71433481688 ms_run[1]:index=36 null null null null 0.98366,0.98677,0.98606,0.98567,0.97685,0.97706,0.96534,0.98540 -PSM NEKSEEEQSSASVK 38 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9875149647394816 null null 2 776.35913 776.3602803168801 ms_run[1]:index=37 null null null null 0.98915,0.98944,0.98834,0.98835,0.98850,0.98888,0.97847,0.98778,0.98852,0.98666,0.98830,0.98710,0.98650,0.98822 -PSM NNTVTPGGKPGGK 39 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.946726496730532 null null 2 613.82745 613.8280178168801 ms_run[1]:index=38 null null null null 0.93242,0.80678,0.95406,0.96786,0.88768,0.96598,0.96954,0.96820,0.96772,0.96757,0.96759,0.96293,0.96766 -PSM HNGEEEEETHK 40 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.4023066883285841 null null 2 674.2913 669.7814653168799 ms_run[1]:index=39 null null null null 0.79198,0.79514,0.76636,0.39427,0.42610,0.40046,0.40083,0.39425,0.44152,0.77926,0.78835 -PSM HDSVEER 41 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9554774761199951 null null 2 436.19864 436.1988558168801 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4.1.1.dev15+gcedfaa7.d20240625] 0.7837637743124595 null null 2 693.391 693.39098581688 ms_run[1]:index=87 null null null null 0.88423,0.56842,0.49764,0.48800,0.69792,0.86291,0.88665,0.88700,0.88647,0.87839,0.87596,0.88848 -PSM VTLTNHK 89 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9906119257211685 null null 2 406.73508 406.73486881688 ms_run[1]:index=88 null null null null 0.99117,0.99167,0.99138,0.98946,0.99058,0.99082,0.98972 -PSM KQVHPDTGLSSK 90 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.784689323260234 null null 2 648.8487 648.84895431688 ms_run[1]:index=89 null null null null 0.88510,0.86906,0.88436,0.60227,0.56352,0.73759,0.86867,0.88519,0.88925,0.58474,0.65597,0.88862 -PSM ALHVNNDR 91 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9739643534024557 null null 2 469.74402 469.74376481687995 ms_run[1]:index=90 null null null null 0.98300,0.94303,0.94576,0.98170,0.98200,0.98309,0.98087,0.98429 -PSM HQGVDVSQGQK 92 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.2755244250098864 null null 2 602.2881 591.7967268168799 ms_run[1]:index=91 null null null null 0.81014,0.61340,0.85479,0.55058,0.51206,0.80981,0.52666,0.74098,0.72937,0.84537,0.84671 -PSM KDQLADAR 93 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9833353890313042 null null 2 458.74606 458.74597381688005 ms_run[1]:index=92 null null null null 0.98578,0.98789,0.96864,0.98753,0.98707,0.98619,0.97211,0.98784 -PSM AGM+15.995THLVR 94 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9909310738245646 null null 2 450.73972 450.73963331688 ms_run[1]:index=93 null null null null 0.98624,0.99125,0.99075,0.99034,0.99038,0.99374,0.99342,0.99157 -PSM VC+57.021ETDTEC+57.021EAK 95 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8007588014006615 null null 2 671.7649 671.26848431688 ms_run[1]:index=94 null null null null 0.85310,0.86264,0.63520,0.51281,0.54561,0.89137,0.87732,0.89623,0.89416,0.85729,0.88848 -PSM DNEEETTDDPRK 96 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9748788430140569 null null 2 724.8101 724.81041531688 ms_run[1]:index=95 null null null null 0.97278,0.97866,0.98283,0.94063,0.97179,0.98396,0.98175,0.97949,0.97996,0.98068,0.96405,0.97450 -PSM LATENSTQAQSK 97 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8541486240350283 null null 2 639.3202 639.32022231688 ms_run[1]:index=96 null null null null 0.91946,0.88310,0.64405,0.91759,0.61508,0.70209,0.92141,0.92149,0.91321,0.92107,0.90086,0.92215 -PSM SVHELEK 98 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9886416047811508 null null 2 421.2242 421.22434231688004 ms_run[1]:index=97 null null null null 0.98951,0.98664,0.98892,0.98538,0.98991,0.98926,0.99082 -PSM SGTATAANPAEM+15.995YK 99 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6758072773615519 null null 2 714.3115 714.32719081688 ms_run[1]:index=98 null null null null 0.49935,0.43461,0.57078,0.53960,0.56327,0.81141,0.63182,0.67101,0.83289,0.79074,0.74597,0.62813,0.74957,0.83457 -PSM +42.011SGEELRK 100 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.15170641077889335 null null 2 437.25616 430.7272493168801 ms_run[1]:index=99 null null null null 0.85811,0.91444,0.88994,0.69713,0.91029,0.88104,0.68493,0.87894 -PSM TSYAQHQQVR 101 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.989588509906422 null null 2 609.3046 609.3047148168799 ms_run[1]:index=100 null null null null 0.99056,0.99011,0.98729,0.98997,0.99053,0.98848,0.98996,0.98965,0.99105,0.98859 -PSM NDEELNK 102 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9784338027238846 null null 2 431.2012 431.20106381688004 ms_run[1]:index=101 null null null null 0.98508,0.98284,0.98438,0.97530,0.97293,0.96303,0.97950 -PSM GGSLPQNHLHGH 103 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7780202948130094 null null 2 627.3102 627.3103353168799 ms_run[1]:index=102 null null null null 0.88073,0.88552,0.88639,0.53989,0.48982,0.59155,0.75677,0.88470,0.79813,0.81800,0.81249,0.88578 -PSM EESGKPQHVTVK 104 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9577845564255347 null null 2 669.8538 669.85423681688 ms_run[1]:index=103 null null null null 0.97224,0.97328,0.97316,0.97085,0.97283,0.78519,0.97378,0.96353,0.97323,0.97306,0.97223,0.97381 -PSM NSYTN+0.984GHSSDK 105 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6759249443809191 null null 2 605.7616 605.75217631688 ms_run[1]:index=104 null null null null 0.80744,0.47209,0.48691,0.43885,0.55379,0.57064,0.61858,0.83322,0.82685,0.83470,0.83499 -PSM APTQGEC+57.021HC+57.021DQTF 106 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6652015820145607 null null 2 775.8415 775.8035578168799 ms_run[1]:index=105 null null null null 0.42189,0.79374,0.76732,0.44555,0.50619,0.52009,0.46332,0.59417,0.82448,0.66210,0.82893,0.82902,0.82790 -PSM NVHELEK 107 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9881609752774239 null null 2 434.7295 434.72979181688004 ms_run[1]:index=106 null null null null 0.98844,0.98742,0.98892,0.98666,0.98955,0.98984,0.98553 -PSM YPNHSVDR 108 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9701713191138374 null null 2 494.2362 494.23577281688 ms_run[1]:index=107 null null null null 0.98136,0.88748,0.97896,0.98037,0.98181,0.97936,0.98056,0.98167 -PSM NKEGEVDYAK 109 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8123747543855147 null null 2 576.78033 576.7802103168799 ms_run[1]:index=108 null null null null 0.90083,0.90001,0.89895,0.59818,0.57671,0.56759,0.90301,0.89488,0.90020,0.89448 -PSM LRPEPNTGK 110 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.052142149209976174 null null 2 499.27567 506.28271881688005 ms_run[1]:index=109 null null null null 0.96482,0.96376,0.96742,0.96250,0.96909,0.84115,0.96040,0.94795,0.93244 -PSM NN+0.984EELNK 111 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20876559987664223 null null 2 421.71188 431.20106381688004 ms_run[1]:index=110 null null null null 0.89154,0.89164,0.89013,0.88795,0.88142,0.61297,0.87860 -PSM PHESNYEEDGK 112 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3362173897524675 null null 2 646.7648 652.77311331688 ms_run[1]:index=111 null null null null 0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 -PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 -PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 -PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 -PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 -PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 -PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 -PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 -PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 -PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 -PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 -PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 -PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 -PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 -PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 -PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 -PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 diff --git a/foo2.mztab b/foo2.mztab deleted file mode 100644 index c95f7791..00000000 --- a/foo2.mztab +++ /dev/null @@ -1,189 +0,0 @@ -MTD mzTab-version 1.0.0 -MTD mzTab-mode Summary -MTD mzTab-type Identification -MTD description Casanovo identification file foo2 -MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] -MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] -MTD fixed_mod[1]-site C -MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[1]-site N -MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[2]-site Q -MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] -MTD variable_mod[3]-site M -MTD variable_mod[4] [UNIMOD, UNIMOD:385, Ammonia-loss, ] -MTD variable_mod[4]-site N-term -MTD variable_mod[5] [UNIMOD, UNIMOD:1, Acetyl, ] -MTD variable_mod[5]-site N-term -MTD variable_mod[6] [UNIMOD, UNIMOD:5, Carbamyl, ] -MTD variable_mod[6]-site N-term -MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt -MTD software[1]-setting[2] config_filename = default -MTD software[1]-setting[3] precursor_mass_tol = 50.0 -MTD software[1]-setting[4] isotope_error_range = (0, 1) -MTD software[1]-setting[5] min_peptide_len = 6 -MTD software[1]-setting[6] predict_batch_size = 1024 -MTD software[1]-setting[7] n_beams = 1 -MTD software[1]-setting[8] top_match = 1 -MTD software[1]-setting[9] accelerator = auto -MTD software[1]-setting[10] devices = None -MTD software[1]-setting[11] random_seed = 454 -MTD software[1]-setting[12] n_log = 1 -MTD software[1]-setting[13] tb_summarywriter = None -MTD software[1]-setting[14] save_top_k = 5 -MTD software[1]-setting[15] model_save_folder_path = -MTD software[1]-setting[16] val_check_interval = 50000 -MTD software[1]-setting[17] n_peaks = 150 -MTD software[1]-setting[18] min_mz = 50.0 -MTD software[1]-setting[19] max_mz = 2500.0 -MTD software[1]-setting[20] min_intensity = 0.01 -MTD software[1]-setting[21] remove_precursor_tol = 2.0 -MTD software[1]-setting[22] max_charge = 10 -MTD software[1]-setting[23] dim_model = 512 -MTD software[1]-setting[24] n_head = 8 -MTD software[1]-setting[25] dim_feedforward = 1024 -MTD software[1]-setting[26] n_layers = 9 -MTD software[1]-setting[27] dropout = 0.0 -MTD software[1]-setting[28] dim_intensity = None -MTD software[1]-setting[29] max_length = 100 -MTD software[1]-setting[30] warmup_iters = 100000 -MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 -MTD software[1]-setting[32] learning_rate = 0.0005 -MTD software[1]-setting[33] weight_decay = 1e-05 -MTD software[1]-setting[34] train_label_smoothing = 0.01 -MTD software[1]-setting[35] train_batch_size = 32 -MTD software[1]-setting[36] max_epochs = 30 -MTD software[1]-setting[37] num_sanity_val_steps = 0 -MTD software[1]-setting[38] calculate_precision = False -MTD software[1]-setting[40] n_workers = 0 -MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf -PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores -PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 -PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 -PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 -PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 -PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 -PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 -PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 -PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 -PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 -PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 -PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 -PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 -PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 -PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 -PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 -PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9672952890396118 null null 2 614.33795 614.33821831688 ms_run[1]:index=15 null null null null 0.97399,0.97959,0.97837,0.97845,0.96474,0.84979,0.97928,0.97613,0.97886,0.97760,0.97960,0.97994 -PSM LQEEERER 17 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.975036793284946 null null 2 544.77 544.77017681688 ms_run[1]:index=16 null null null null 0.91222,0.98079,0.98579,0.98252,0.98429,0.98225,0.98285,0.98220 -PSM TRGHESEMK 18 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1844959855079651 null null 2 539.25323 537.75346831688 ms_run[1]:index=17 null null null null 0.90297,0.90465,0.82135,0.90041,0.64139,0.62194,0.66087,0.89718,0.90124 -PSM +42.011KVEDPPRK 19 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.24581749439239498 null null 2 507.26154 505.78509881688007 ms_run[1]:index=18 null null null null 0.77158,0.66196,0.86775,0.87090,0.70578,0.61787,0.85217,0.69678,0.62489 -PSM TESPAEGKQEEEK 20 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.868788189121655 null null 2 731.3395 731.3388133168802 ms_run[1]:index=19 null null null null 0.92347,0.91621,0.74657,0.61987,0.87546,0.65200,0.92947,0.92629,0.93151,0.92995,0.92921,0.92534,0.92826 -PSM LVEEETKK 21 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879584113756815 null null 2 488.27112 488.27148531688005 ms_run[1]:index=20 null null null null 0.98623,0.98691,0.98852,0.98742,0.98734,0.98694,0.99077,0.98849 -PSM KAETLGEK 22 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9864536391364204 null null 2 438.24524 438.24527081688 ms_run[1]:index=21 null null null null 0.98740,0.98704,0.98770,0.98844,0.98931,0.98661,0.98774,0.97524 -PSM C+57.021LKPNETK 23 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9895809359020658 null null 2 495.25775 495.25785531688 ms_run[1]:index=22 null null null null 0.98927,0.98929,0.98595,0.99043,0.99001,0.99081,0.98784,0.99231 -PSM GHQALER 24 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9861482679843903 null null 2 405.71454 405.71447681688 ms_run[1]:index=23 null null null null 0.98369,0.97763,0.98807,0.98786,0.98838,0.98693,0.98818 -PSM TNNLRPK 25 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9859854802489281 null null 2 421.74548 421.74577181688005 ms_run[1]:index=24 null null null null 0.98893,0.99008,0.98974,0.98259,0.98795,0.97375,0.98633 -PSM +43.006DTPGHATPGHGAGTQER 26 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.22608531070382976 null null 2 867.40045 866.39330131688 ms_run[1]:index=25 null null null null 0.85561,0.57927,0.49126,0.50495,0.70489,0.76038,0.75372,0.53050,0.87917,0.87740,0.88139,0.87799,0.88406,0.88016,0.88217,0.87672,0.82864,0.77355 -PSM KSYTTPK 27 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8933427818119526 null null 2 412.72778 412.72925231688004 ms_run[1]:index=26 null null null null 0.93932,0.94376,0.93479,0.61684,0.94099,0.93574,0.89386 -PSM VLEGHAEK 28 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879539277818468 null null 2 441.73788 441.73761731688 ms_run[1]:index=27 null null null null 0.98716,0.98573,0.98970,0.98983,0.98921,0.98323,0.98926,0.98847 -PSM LQHEATAATQK 29 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9673882275819778 null null 2 599.3142 599.31474381688 ms_run[1]:index=28 null null null null 0.97810,0.97690,0.97761,0.96875,0.88905,0.98107,0.97901,0.94171,0.98001,0.97853,0.97914 -PSM KEAPAPPK 30 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.99110433128145 null null 2 419.24496 419.24507831688004 ms_run[1]:index=29 null null null null 0.98966,0.99341,0.99059,0.99097,0.99120,0.99191,0.99078,0.99143 -PSM ERDELR 31 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9874146069799151 null null 2 409.2106 409.2117663168801 ms_run[1]:index=30 null null null null 0.98921,0.98706,0.98802,0.98241,0.98891,0.98739 -PSM EVLHANNR 32 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8818797965844473 null null 2 476.75156 476.75158981687997 ms_run[1]:index=31 null null null null 0.93772,0.73514,0.67541,0.93265,0.93705,0.93603,0.93502,0.91176 -PSM NNTLTPNKPNK 33 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1514618446429571 null null 2 613.8276 620.83584181688 ms_run[1]:index=32 null null null null 0.90068,0.80453,0.91917,0.67357,0.80102,0.91849,0.91801,0.71365,0.91622,0.90961,0.78907 -PSM MQEHMR 34 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894828966685704 null null 2 416.18372 416.18364081688 ms_run[1]:index=33 null null null null 0.98712,0.98906,0.99189,0.98772,0.99073,0.98986 -PSM HNSYTAC+57.021ETHK 35 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8552879715959231 null null 2 674.29083 674.29094231688 ms_run[1]:index=34 null null null null 0.91161,0.92276,0.92215,0.75983,0.57698,0.64840,0.90726,0.92049,0.92356,0.92284,0.92449 -PSM WAPGHATPFSDESSSR 36 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43844590730526867 null null 2 867.4 866.3897028168802 ms_run[1]:index=35 null null null null 0.62368,0.35030,0.34498,0.43399,0.63293,0.39463,0.54277,0.45963,0.77829,0.76285,0.61244,0.56565,0.66891,0.77050,0.38220,0.45175 -PSM GDDETLHK 37 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9814771148893568 null null 2 457.71384 457.71433481688 ms_run[1]:index=36 null null null null 0.98366,0.98677,0.98606,0.98567,0.97685,0.97706,0.96534,0.98540 -PSM NEKSEEEQSSASVK 38 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9875149647394816 null null 2 776.35913 776.3602803168801 ms_run[1]:index=37 null null null null 0.98915,0.98944,0.98834,0.98835,0.98850,0.98888,0.97847,0.98778,0.98852,0.98666,0.98830,0.98710,0.98650,0.98822 -PSM NNTVTPGGKPGGK 39 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.946726496730532 null null 2 613.82745 613.8280178168801 ms_run[1]:index=38 null null null null 0.93242,0.80678,0.95406,0.96786,0.88768,0.96598,0.96954,0.96820,0.96772,0.96757,0.96759,0.96293,0.96766 -PSM HNGEEEEETHK 40 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.4023066883285841 null null 2 674.2913 669.7814653168799 ms_run[1]:index=39 null null null null 0.79198,0.79514,0.76636,0.39427,0.42610,0.40046,0.40083,0.39425,0.44152,0.77926,0.78835 -PSM HDSVEER 41 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9554774761199951 null null 2 436.19864 436.1988558168801 ms_run[1]:index=40 null null null null 0.94772,0.95530,0.92708,0.94280,0.96933,0.95420,0.97425 -PSM EGGQVASMEEEK 42 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.48210483216322386 null null 2 648.29266 647.28499981688 ms_run[1]:index=41 null null null null 0.39005,0.43086,0.42453,0.34300,0.64313,0.48547,0.75237,0.73883,0.36843,0.39590,0.47632,0.52967 -PSM AVTKYTSSK 43 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865922451019287 null null 2 492.77188 492.77164831688003 ms_run[1]:index=42 null null null null 0.98637,0.98900,0.98957,0.98818,0.98921,0.98818,0.98726,0.97004,0.98958 -PSM TKYTSSK 44 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.977924220263958 null null 2 407.71896 407.71888431688 ms_run[1]:index=43 null null null null 0.98495,0.98298,0.98361,0.98325,0.98555,0.93525,0.98402 -PSM SSFSQHAR 45 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9911030067337884 null null 2 460.22247 460.22266531687995 ms_run[1]:index=44 null null null null 0.99131,0.99140,0.99089,0.99075,0.99078,0.99212,0.99089,0.99124 -PSM SYTSSDTAHK 46 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8599473617293618 null null 2 548.73834 548.7489013168799 ms_run[1]:index=45 null null null null 0.92316,0.92249,0.69404,0.88593,0.67066,0.74161,0.92698,0.92628,0.91877,0.92507 -PSM GTGHTDAENEEVK 47 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6680682482463973 null null 2 693.80896 693.81021881688 ms_run[1]:index=46 null null null null 0.82323,0.80847,0.54724,0.46113,0.45871,0.66241,0.80819,0.56945,0.81953,0.69455,0.49138,0.58402,0.79585 -PSM NEKSEETTEEEVK 48 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7301746702619961 null null 2 776.3595 776.3546553168801 ms_run[1]:index=47 null null null null 0.85148,0.85378,0.52621,0.52819,0.47325,0.67612,0.85314,0.60486,0.86022,0.85298,0.83021,0.68631,0.76565 -PSM KQEEEPNEDTASTSK 49 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9210587590932846 null null 2 846.8801 846.88156881688 ms_run[1]:index=48 null null null null 0.94103,0.95696,0.85467,0.95359,0.83247,0.95710,0.95140,0.93730,0.90773,0.95238,0.95063,0.87036,0.95098,0.81020,0.95436 -PSM NKPGVYTK 50 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9890277054574754 null null 2 453.75558 453.75580581688007 ms_run[1]:index=49 null null null null 0.98844,0.98980,0.99009,0.98958,0.98979,0.98914,0.98524,0.98951 -PSM RPHETGPK 51 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.2289043515920639 null null 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4.1.1.dev15+gcedfaa7.d20240625] -0.10741639137268066 null null 2 464.76294 457.75633731688 ms_run[1]:index=54 null null null null 0.94085,0.93904,0.90654,0.79190,0.71994,0.92227,0.93329,0.93771 -PSM KSTNQLPR 56 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.21645448936356437 null null 2 469.7016 472.2696113168801 ms_run[1]:index=55 null null null null 0.88299,0.73059,0.51941,0.66659,0.86420,0.88391,0.88618,0.73064 -PSM TDGTTESEAAEAK 57 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8022329785994121 null null 2 655.29083 655.2913233168799 ms_run[1]:index=56 null null null null 0.89606,0.89051,0.59173,0.53286,0.66625,0.58621,0.89531,0.87847,0.89276,0.89359,0.89336,0.82298,0.89563 -PSM KQHSLLK 58 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9910597279667854 null null 2 427.26633 427.26634481688 ms_run[1]:index=57 null null null null 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4.1.1.dev15+gcedfaa7.d20240625] 0.8123747543855147 null null 2 576.78033 576.7802103168799 ms_run[1]:index=108 null null null null 0.90083,0.90001,0.89895,0.59818,0.57671,0.56759,0.90301,0.89488,0.90020,0.89448 -PSM LRPEPNTGK 110 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.052142149209976174 null null 2 499.27567 506.28271881688005 ms_run[1]:index=109 null null null null 0.96482,0.96376,0.96742,0.96250,0.96909,0.84115,0.96040,0.94795,0.93244 -PSM NN+0.984EELNK 111 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20876559987664223 null null 2 421.71188 431.20106381688004 ms_run[1]:index=110 null null null null 0.89154,0.89164,0.89013,0.88795,0.88142,0.61297,0.87860 -PSM PHESNYEEDGK 112 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3362173897524675 null null 2 646.7648 652.77311331688 ms_run[1]:index=111 null null null null 0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 -PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 -PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 -PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 -PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 -PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 -PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 -PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 -PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 -PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 -PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 -PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 -PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 -PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 -PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 -PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 -PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 From dccb729059888772b0fc0c41bf9f014954c18aac Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 31 Jul 2024 18:29:22 +0000 Subject: [PATCH 06/36] Generate new screengrabs with rich-codex --- docs/images/evaluate-help.svg | 135 +++++++-------------------- docs/images/help.svg | 168 +++++++++++++++++----------------- docs/images/sequence-help.svg | 142 ++++++++++++++-------------- 3 files changed, 187 insertions(+), 258 deletions(-) diff --git a/docs/images/evaluate-help.svg b/docs/images/evaluate-help.svg index 2f770e2e..661f0efe 100644 --- a/docs/images/evaluate-help.svg +++ b/docs/images/evaluate-help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - - $ casanovo evaluate --help - -Usage:casanovo evaluate [OPTIONS] ANNOTATED_PEAK_PATH...                       - - Evaluate de novo peptide sequencing performance.                                - ANNOTATED_PEAK_PATH must be one or more annoated MGF files, such as those       - provided by MassIVE-KB.                                                         - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*  ANNOTATED_PEAK_PATH    FILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--model-mFILE                        The model weights (.ckpt file). │ -│                                              If not provided, Casanovo will  │ -│                                              try to download the latest      │ -│                                              release.                        │ -│--output-oFILE                        The mzTab file to which results │ -│                                              will be written.                │ -│--config-cFILE                        The YAML configuration file     │ -│                                              overriding the default options. │ -│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ -│                                              logging messages. Log files are │ -│                                              always set to 'debug'.          │ -│--help-h  Show this message and exit.     │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo evaluate --help + +Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     + +Try'casanovo -h'for help +╭─ Error ──────────────────────────────────────────────────────────────────────╮ +│ No such command 'evaluate'.                                                  │ +╰──────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/help.svg b/docs/images/help.svg index 80d63c7e..dbdc05e0 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - + - + - - $ casanovo --help - -Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     - - ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  - ┃                                  Casanovo                                  ┃  - ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  - Casanovo de novo sequences peptides from tandem mass spectra using a            - Transformer model. Casanovo currently supports mzML, mzXML, and MGF files for   - de novo sequencing and annotated MGF files, such as those from MassIVE-KB, for  - training new models.                                                            - - Links:                                                                          - - • Documentation: https://casanovo.readthedocs.io                               - • Official code repository: https://github.com/Noble-Lab/casanovo              - - If you use Casanovo in your work, please cite:                                  - - • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   -mass spectrometry peptide sequencing with a transformer model. Proceedings   -of the 39th International Conference on Machine Learning - ICML '22 (2022)   -doi:10.1101/2022.02.07.479481.                                               - -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--help-h    Show this message and exit.                                    │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────╮ -│configure Generate a Casanovo configuration file to customize.              │ -│evaluate  Evaluate de novo peptide sequencing performance.                  │ -│sequence  De novo sequence peptides from tandem mass spectra.               │ -│train     Train a Casanovo model on your own data.                          │ -│version   Get the Casanovo version information                              │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo --help + +Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     + + ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  + ┃                                  Casanovo                                  ┃  + ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  + Casanovo de novo sequences peptides from tandem mass spectra using a            + Transformer model. Casanovo currently supports mzML, mzXML, and MGF files for   + de novo sequencing and annotated MGF files, such as those from MassIVE-KB, for  + training new models.                                                            + + Links:                                                                          + + • Documentation: https://casanovo.readthedocs.io                               + • Official code repository: https://github.com/Noble-Lab/casanovo              + + If you use Casanovo in your work, please cite:                                  + + • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   +mass spectrometry peptide sequencing with a transformer model. Proceedings   +of the 39th International Conference on Machine Learning - ICML '22 (2022)   +doi:10.1101/2022.02.07.479481.                                               + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--help-h    Show this message and exit.                                    │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────╮ +│configure Generate a Casanovo configuration file to customize.              │ +│sequence  De novo sequence peptides from tandem mass spectra.               │ +│train     Train a Casanovo model on your own data.                          │ +│version   Get the Casanovo version information                              │ +╰──────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/sequence-help.svg b/docs/images/sequence-help.svg index 6635cfaa..e8a0d6d7 100644 --- a/docs/images/sequence-help.svg +++ b/docs/images/sequence-help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ casanovo sequence --help - -Usage:casanovo sequence [OPTIONS] PEAK_PATH...                                 - - De novo sequence peptides from tandem mass spectra.                             - PEAK_PATH must be one or more mzMl, mzXML, or MGF files from which to sequence  - peptides.                                                                       - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*  PEAK_PATH    FILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--model-mFILE                        The model weights (.ckpt file). │ -│                                              If not provided, Casanovo will  │ -│                                              try to download the latest      │ -│                                              release.                        │ -│--output-oFILE                        The mzTab file to which results │ -│                                              will be written.                │ -│--config-cFILE                        The YAML configuration file     │ -│                                              overriding the default options. │ -│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ -│                                              logging messages. Log files are │ -│                                              always set to 'debug'.          │ -│--help-h  Show this message and exit.     │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo sequence --help + +Usage:casanovo sequence [OPTIONS] PEAK_PATH...                                 + + De novo sequence peptides from tandem mass spectra.                             + PEAK_PATH must be one or more mzML, mzXML, or MGF files from which to sequence  + peptides.                                                                       + +╭─ Arguments ──────────────────────────────────────────────────────────────────╮ +│*  PEAK_PATH    FILE[required]│ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--evaluate-e  Run in evaluation mode.         │ +│--model-mFILE                        The model weights (.ckpt file). │ +│                                              If not provided, Casanovo will  │ +│                                              try to download the latest      │ +│                                              release.                        │ +│--output-oFILE                        The mzTab file to which results │ +│                                              will be written.                │ +│--config-cFILE                        The YAML configuration file     │ +│                                              overriding the default options. │ +│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ +│                                              logging messages. Log files are │ +│                                              always set to 'debug'.          │ +│--help-h  Show this message and exit.     │ +╰──────────────────────────────────────────────────────────────────────────────╯ + From 5879b0a93b0b9ef8f13b7c54a16ce32788675087 Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Fri, 2 Aug 2024 11:52:26 +0200 Subject: [PATCH 07/36] Update paper reference (#361) --- README.md | 2 +- docs/index.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 533c76e2..35b7c646 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ If you use Casanovo in your work, please cite the following publications: - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mass spectrometry peptide sequencing with a transformer model. in *Proceedings of the 39th International Conference on Machine Learning - ICML '22* vol. 162 25514–25522 (PMLR, 2022). [https://proceedings.mlr.press/v162/yilmaz22a.html](https://proceedings.mlr.press/v162/yilmaz22a.html) -- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *bioRxiv* (2023). [doi:10.1101/2023.01.03.522621](https://doi.org/10.1101/2023.01.03.522621) +- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) ## Documentation diff --git a/docs/index.md b/docs/index.md index 2283aeb2..3dd77622 100644 --- a/docs/index.md +++ b/docs/index.md @@ -7,7 +7,7 @@ If you use Casanovo in your work, please cite the following publications: - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mass spectrometry peptide sequencing with a transformer model. in *Proceedings of the 39th International Conference on Machine Learning - ICML '22* vol. 162 25514–25522 (PMLR, 2022). [https://proceedings.mlr.press/v162/yilmaz22a.html](https://proceedings.mlr.press/v162/yilmaz22a.html) -- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *bioRxiv* (2023). [doi:10.1101/2023.01.03.522621](https://doi.org/10.1101/2023.01.03.522621) +- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) ```{toctree} --- From f792527e07f60f3eebef45773fccc59b4f92614b Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Tue, 6 Aug 2024 08:47:53 +0200 Subject: [PATCH 08/36] Bug report template (#360) * bug report template * punctuation, hardware description item * Restrict NumPy to pre-2.0 (#344) * Restrict NumPy to pre-2.0 * Update changelog * Update paper reference (#361) --------- Co-authored-by: Lilferrit --- .github/ISSUE_TEMPLATE/bug_report_template.md | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/bug_report_template.md diff --git a/.github/ISSUE_TEMPLATE/bug_report_template.md b/.github/ISSUE_TEMPLATE/bug_report_template.md new file mode 100644 index 00000000..cf4c487c --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report_template.md @@ -0,0 +1,55 @@ +--- +name: Bug Report +about: Submit a Casanovo Bug Report +labels: bug +--- + +## Describe the Issue +A clear and concise description of what the issue/bug is. + +## Steps To Reproduce +Steps to reproduce the incorrect behavior. + +## Expected Behavior +A clear and concise description of what you expected to happen. + +## Terminal Output (If Applicable) +Provide any applicable console output in between the tick marks below. + +``` + +``` + +## Environment: +- OS: [e.g. Windows 11, Windows 10, macOS 14, Ubuntu 24.04] +- Casanovo Version: [e.g. 4.2.1] +- Hardware Used (CPU or GPU, if GPU also GPU model and CUDA version): [e.g. GPU: NVIDIA GeForce RTX 2070, CUDA Version: 12.5] + +### Checking GPU Version + +The GPU model can be checked by typing `nvidia-smi` into a terminal/console window. +An example of how to use this command is shown below. +In this case, the CUDA version is 12.5 and the GPU model is GeForce RTX 2070. + + +``` +(casanovo_env) C:\Users\\OneDrive\Documents\casanovo>nvidia-smi +Fri Aug 2 12:34:57 2024 ++-----------------------------------------------------------------------------------------+ +| NVIDIA-SMI 555.99 Driver Version: 555.99 CUDA Version: 12.5 | +|-----------------------------------------+------------------------+----------------------+ +| GPU Name Driver-Model | Bus-Id Disp.A | Volatile Uncorr. ECC | +| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. | +| | | MIG M. | +|=========================================+========================+======================| +| 0 NVIDIA GeForce RTX 2070 ... WDDM | 00000000:01:00.0 On | N/A | +| N/A 60C P8 16W / 90W | 1059MiB / 8192MiB | 0% Default | +| | | N/A | ++-----------------------------------------+------------------------+----------------------+ +``` + +## Additional Context +Add any other context about the problem here. + +## Attach Files +Please attach all input files used and the full Casanovo log file. From bf1e5a36b8f3b73805d1354339562aed9051f4de Mon Sep 17 00:00:00 2001 From: Gwenneth Straub Date: Tue, 6 Aug 2024 00:10:59 -0700 Subject: [PATCH 09/36] upgrade codecove to v4 (#364) --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 7e79b5a3..1c74a29d 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -42,7 +42,7 @@ jobs: run: | pytest --cov=casanovo tests/ - name: Upload coverage to codecov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 with: token: ${{ secrets.CODECOV_TOKEN }} fail_ci_if_error: true From 4c14b940d22894dab89d1a751be04c3fe657b465 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 6 Aug 2024 14:03:19 -0700 Subject: [PATCH 10/36] implemen eval mode at model runner level, fix unit test --- casanovo/data/datasets.py | 21 +-- casanovo/denovo/dataloaders.py | 20 +- casanovo/denovo/model.py | 76 ++------ casanovo/denovo/model_runner.py | 44 ++++- tests/test_integration.py | 35 +--- tests/unit_tests/test_runner.py | 8 +- tests/unit_tests/test_unit.py | 325 ++++++++++++++++++++++++++++++-- 7 files changed, 378 insertions(+), 151 deletions(-) diff --git a/casanovo/data/datasets.py b/casanovo/data/datasets.py index bd3d93af..3917a2c8 100644 --- a/casanovo/data/datasets.py +++ b/casanovo/data/datasets.py @@ -83,11 +83,12 @@ def __getitem__( The unique spectrum identifier, formed by its original peak file and identifier (index or scan number) therein. """ - mz_array, int_array, precursor_mz, precursor_charge = self.index[idx] + mz_array, int_array, precursor_mz, precursor_charge = self.index[idx][ + :4 + ] spectrum = self._process_peaks( mz_array, int_array, precursor_mz, precursor_charge ) - return ( spectrum, precursor_mz, @@ -235,9 +236,7 @@ def __init__( random_state=random_state, ) - def __getitem__( - self, idx: int - ) -> Tuple[torch.Tensor, float, int, Tuple[str, str], str]: + def __getitem__(self, idx: int) -> Tuple[torch.Tensor, float, int, str]: """ Return the annotated MS/MS spectrum with the given index. @@ -254,9 +253,6 @@ def __getitem__( The precursor m/z. precursor_charge : int The precursor charge. - spectrum_id: Tuple[str, str] - The unique spectrum identifier, formed by its original peak file and - identifier (index or scan number) therein. annotation : str The peptide annotation of the spectrum. """ @@ -270,11 +266,4 @@ def __getitem__( spectrum = self._process_peaks( mz_array, int_array, precursor_mz, precursor_charge ) - - return ( - spectrum, - precursor_mz, - precursor_charge, - self.get_spectrum_id(idx), - peptide, - ) + return spectrum, precursor_mz, precursor_charge, peptide diff --git a/casanovo/denovo/dataloaders.py b/casanovo/denovo/dataloaders.py index 9a8b1e32..fe5d6237 100644 --- a/casanovo/denovo/dataloaders.py +++ b/casanovo/denovo/dataloaders.py @@ -175,8 +175,8 @@ def predict_dataloader(self) -> torch.utils.data.DataLoader: def prepare_batch( - batch: List[Tuple[torch.Tensor, float, int, str, Optional[str]]] -) -> Tuple[torch.Tensor, torch.Tensor, np.ndarray, np.ndarray | None]: + batch: List[Tuple[torch.Tensor, float, int, str]] +) -> Tuple[torch.Tensor, torch.Tensor, np.ndarray]: """ Collate MS/MS spectra into a batch. @@ -185,11 +185,10 @@ def prepare_batch( Parameters ---------- - batch : List[Tuple[torch.Tensor, float, int, str, Optional[str]]] + batch : List[Tuple[torch.Tensor, float, int, str]] A batch of data from an AnnotatedSpectrumDataset, consisting of for each spectrum (i) a tensor with the m/z and intensity peak values, (ii), the - precursor m/z, (iii) the precursor charge, (iv) the spectrum identifier, - (v) optionally the peptide sequence annotation + precursor m/z, (iii) the precursor charge, (iv) the spectrum identifier. Returns ------- @@ -202,15 +201,8 @@ def prepare_batch( spectrum_ids : np.ndarray The spectrum identifiers (during de novo sequencing) or peptide sequences (during training). - annotations : np.ndarray | None - The peptide annotations of the spectra if provided by the dataset, - None otherwise """ - batch_list = list(zip(*batch)) - spectra, precursor_mzs, precursor_charges, spectrum_ids = batch_list[0:4] - peptide_sequence = ( - None if len(batch_list) <= 4 else np.asarray(batch_list[4]) - ) + spectra, precursor_mzs, precursor_charges, spectrum_ids = list(zip(*batch)) spectra = torch.nn.utils.rnn.pad_sequence(spectra, batch_first=True) precursor_mzs = torch.tensor(precursor_mzs) precursor_charges = torch.tensor(precursor_charges) @@ -218,4 +210,4 @@ def prepare_batch( precursors = torch.vstack( [precursor_masses, precursor_charges, precursor_mzs] ).T.float() - return spectra, precursors, np.asarray(spectrum_ids), peptide_sequence + return spectra, precursors, np.asarray(spectrum_ids) diff --git a/casanovo/denovo/model.py b/casanovo/denovo/model.py index aae8d925..77df6df5 100644 --- a/casanovo/denovo/model.py +++ b/casanovo/denovo/model.py @@ -748,7 +748,7 @@ def training_step( torch.Tensor The loss of the training step. """ - pred, truth = self._forward_step(batch[0], batch[1], batch[3]) + pred, truth = self._forward_step(*batch) pred = pred[:, :-1, :].reshape(-1, self.decoder.vocab_size + 1) if mode == "train": loss = self.celoss(pred, truth.flatten()) @@ -773,7 +773,7 @@ def validation_step( ---------- batch : Tuple[torch.Tensor, torch.Tensor, List[str]] A batch of (i) MS/MS spectra, (ii) precursor information, (iii) - spectrum identifiers, (iv) peptide sequence annotations + peptide sequences. Returns ------- @@ -781,15 +781,14 @@ def validation_step( The loss of the validation step. """ # Record the loss. - forward_step = self.forward(batch[0], batch[1]) loss = self.training_step(batch, mode="valid") if not self.calculate_precision: - return loss, self._get_predictions(batch, forward_step) + return loss # Calculate and log amino acid and peptide match evaluation metrics from # the predicted peptides. - peptides_pred, peptides_true = [], batch[3] - for spectrum_preds in forward_step: + peptides_pred, peptides_true = [], batch[2] + for spectrum_preds in self.forward(batch[0], batch[1]): for _, _, pred in spectrum_preds: peptides_pred.append(pred) @@ -811,35 +810,26 @@ def validation_step( aa_precision, **log_args, ) - return loss, self._get_predictions(batch, forward_step) + return loss - def _get_predictions( - self, - batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], - forward_res: List[List[Tuple[float, np.ndarray, str]]], + def predict_step( + self, batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], *args ) -> List[Tuple[np.ndarray, float, float, str, float, np.ndarray]]: """ - Extract predictions from model output for a batch of spectra. - - Processes the output from a forward pass of the model to - generate a list of predictions for each spectrum in the batch. + A single prediction step. Parameters ---------- batch : Tuple[torch.Tensor, torch.Tensor, torch.Tensor] - A tuple containing: - - (i) MS/MS spectra data as a torch.Tensor. - - (ii) Precursor information, including charge and m/z values, - - (iii) Spectrum identifiers as a torch.Tensor. - forward_res : List[List[Tuple[float, np.ndarray, str]]] - Output from forward_step + A batch of (i) MS/MS spectra, (ii) precursor information, (iii) + spectrum identifiers as torch Tensors. Returns ------- - List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] - Model predictions for the given batch of spectra containing - spectrum ids, precursor information, peptide sequences as well as - peptide and amino acid-level confidence scores. + predictions: List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] + Model predictions for the given batch of spectra containing spectrum + ids, precursor information, peptide sequences as well as peptide + and amino acid-level confidence scores. """ predictions = [] for ( @@ -851,7 +841,7 @@ def _get_predictions( batch[1][:, 1].cpu().detach().numpy(), batch[1][:, 2].cpu().detach().numpy(), batch[2], - forward_res, + self.forward(batch[0], batch[1]), ): for peptide_score, aa_scores, peptide in spectrum_preds: predictions.append( @@ -867,27 +857,6 @@ def _get_predictions( return predictions - def predict_step( - self, batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], *args - ) -> List[Tuple[np.ndarray, float, float, str, float, np.ndarray]]: - """ - A single prediction step. - - Parameters - ---------- - batch : Tuple[torch.Tensor, torch.Tensor, torch.Tensor] - A batch of (i) MS/MS spectra, (ii) precursor information, (iii) - spectrum identifiers as torch Tensors. - - Returns - ------- - predictions: List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] - Model predictions for the given batch of spectra containing spectrum - ids, precursor information, peptide sequences as well as peptide - and amino acid-level confidence scores. - """ - return self._get_predictions(batch, self.forward(batch[0], batch[1])) - def on_train_epoch_end(self) -> None: """ Log the training loss at the end of each epoch. @@ -956,19 +925,6 @@ def on_predict_batch_end( ), ) - def on_validation_batch_end( - self, - outputs: Tuple[ - torch.Tensor, List[Tuple[np.ndarray, List[str], torch.Tensor]] - ], - *args, - ) -> None: - """ - Write the predicted peptide sequences and amino acid scores to the - output file. - """ - self.on_predict_batch_end(outputs[1]) - def _log_history(self) -> None: """ Write log to console, if requested. diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index f5990097..aed57f0c 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -10,6 +10,7 @@ from pathlib import Path from typing import Iterable, List, Optional, Union +import depthcharge.masses import lightning.pytorch as pl import numpy as np import torch @@ -20,6 +21,7 @@ from ..config import Config from ..data import ms_io from ..denovo.dataloaders import DeNovoDataModule +from ..denovo.evaluate import aa_match_batch, aa_match_metrics from ..denovo.model import Spec2Pep @@ -116,8 +118,35 @@ def train( self.loaders.val_dataloader(), ) + def log_metrics(self, test_index: AnnotatedSpectrumIndex) -> None: + """Log pep_precision and aa_precision + + Calculate and log peptide precision and amino acid precision + based off of model predictions and spectrum annotations + + Parameters + ---------- + test_index : AnnotatedSpectrumIndex + Index containing the annotated spectra used to generate model + predictions + """ + model_output = [psm[0] for psm in self.writer.psms] + spectrum_annotations = [ + test_index[i][4] for i in range(test_index.n_spectra) + ] + aa_precision, _, pep_precision = aa_match_metrics( + *aa_match_batch( + spectrum_annotations, + model_output, + depthcharge.masses.PeptideMass().masses, + ) + ) + + logger.info("Peptide Precision: %f", pep_precision) + logger.info("Amino Acid Precision: %f", aa_precision) + def predict( - self, peak_path: Iterable[str], output: str, evaluate=False + self, peak_path: Iterable[str], output: str, evaluate: bool = False ) -> None: """Predict peptide sequences with a trained Casanovo model. @@ -130,7 +159,7 @@ def predict( The path with the MS data files for predicting peptide sequences. output : str Where should the output be saved? - evaluate: str + evaluate: bool whether to run model evaluation in addition to inference Note: peak_path most point to annotated MS data files when running model evaluation. Files that are not an annotated @@ -151,17 +180,14 @@ def predict( self.initialize_model(train=False) self.model.out_writer = self.writer - test_index = self._get_index( - peak_path, evaluate, "evaluation" if evaluate else "" - ) + test_index = self._get_index(peak_path, evaluate, "") self.writer.set_ms_run(test_index.ms_files) self.initialize_data_module(test_index=test_index) - self.loaders.setup(stage="test", annotated=evaluate) + self.loaders.setup(stage="test", annotated=False) + self.trainer.predict(self.model, self.loaders.test_dataloader()) if evaluate: - self.trainer.validate(self.model, self.loaders.test_dataloader()) - else: - self.trainer.predict(self.model, self.loaders.test_dataloader()) + self.log_metrics(test_index) def initialize_trainer(self, train: bool) -> None: """Initialize the lightning Trainer. diff --git a/tests/test_integration.py b/tests/test_integration.py index 6b2a0b7b..73c3a2d9 100644 --- a/tests/test_integration.py +++ b/tests/test_integration.py @@ -35,7 +35,7 @@ def test_train_and_run( assert result.exit_code == 0 assert model_file.exists() - # Try predicting: + # Finally try predicting: output_filename = tmp_path / "test.mztab" predict_args = [ "sequence", @@ -71,39 +71,6 @@ def test_train_and_run( assert psms.loc[4, "sequence"] == "PEPTLDEK" assert psms.loc[4, "spectra_ref"] == "ms_run[2]:scan=111" - # Finally, try evaluating: - output_filename = tmp_path / "test-eval.mztab" - eval_args = [ - "sequence", - "--model", - str(model_file), - "--config", - tiny_config, - "--output", - str(output_filename), - str(mgf_small), - str(mzml_small), - "--evaluate", - ] - - result = run(eval_args) - assert result.exit_code == 0 - assert output_filename.is_file() - - mztab = pyteomics.mztab.MzTab(str(output_filename)) - # Verify that both input peak files are listed in the metadata. - for i, filename in enumerate(["small.mgf"], 1): - assert f"ms_run[{i}]-location" in mztab.metadata - assert mztab.metadata[f"ms_run[{i}]-location"].endswith(filename) - - # Verify that the spectrum predictions are correct - # and indexed according to the peak input file type. - psms = mztab.spectrum_match_table - assert psms.loc[1, "sequence"] == "LESLLEK" - assert psms.loc[1, "spectra_ref"] == "ms_run[1]:index=0" - assert psms.loc[2, "sequence"] == "PEPTLDEK" - assert psms.loc[2, "spectra_ref"] == "ms_run[1]:index=1" - def test_auxilliary_cli(tmp_path, monkeypatch): """Test the secondary CLI commands""" diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index 96a2738a..6f674c64 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -56,7 +56,7 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): config.max_epochs = 1 config.n_layers = 1 ckpt = tmp_path / "test.ckpt" - output_file = tmp_path / "out" + mztab = tmp_path / "test.mztab" with ModelRunner(config=config) as runner: runner.train([mgf_small], [mgf_small]) @@ -84,7 +84,7 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): with torch.device("meta"): with ModelRunner(other_config, model_filename=str(ckpt)) as runner: with pytest.raises(NotImplementedError) as err: - runner.predict([mgf_small], output_file, evaluate=True) + runner.predict([mgf_small], mztab) assert "meta tensor; no data!" in str(err.value) @@ -96,11 +96,11 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): # Shouldn't work: with ModelRunner(other_config, model_filename=str(ckpt)) as runner: with pytest.raises(RuntimeError): - runner.predict([mgf_small], output_file, evaluate=True) + runner.predict([mgf_small], mztab) # Should work: with ModelRunner(config=config, model_filename=str(ckpt)) as runner: - runner.predict([mgf_small], output_file, evaluate=True) + runner.predict([mgf_small], mztab) def test_save_and_load_weights_deprecated(tmp_path, mgf_small, tiny_config): diff --git a/tests/unit_tests/test_unit.py b/tests/unit_tests/test_unit.py index 2a62000b..120e341a 100644 --- a/tests/unit_tests/test_unit.py +++ b/tests/unit_tests/test_unit.py @@ -1,9 +1,17 @@ import collections +import datetime +import functools +import hashlib import heapq +import io import os +import pathlib import platform +import requests import shutil import tempfile +import unittest +import unittest.mock import einops import github @@ -69,7 +77,172 @@ def test_split_version(): assert version == ("3", "0", "1") -@pytest.mark.skip(reason="Hit rate limit during CI/CD") +class MockResponseGet: + file_content = b"fake model weights content" + + class MockRaw(io.BytesIO): + def read(self, *args, **kwargs): + return super().read(*args) + + def __init__(self): + self.request_counter = 0 + self.is_ok = True + + def raise_for_status(self): + if not self.is_ok: + raise requests.HTTPError + + def __call__(self, url, stream=True, allow_redirects=True): + self.request_counter += 1 + response = unittest.mock.MagicMock() + response.raise_for_status = self.raise_for_status + response.headers = {"Content-Length": str(len(self.file_content))} + response.raw = MockResponseGet.MockRaw(self.file_content) + return response + + +class MockAsset: + def __init__(self, file_name): + self.name = file_name + self.browser_download_url = f"http://example.com/{file_name}" + + +class MockRelease: + def __init__(self, tag_name, assets): + self.tag_name = tag_name + self.assets = [MockAsset(asset) for asset in assets] + + def get_assets(self): + return self.assets + + +class MockRepo: + def __init__( + self, + release_dict={ + "v3.0.0": [ + "casanovo_massivekb.ckpt", + "casanovo_non-enzy.checkpt", + "v3.0.0.zip", + "v3.0.0.tar.gz", + ], + "v3.1.0": ["v3.1.0.zip", "v3.1.0.tar.gz"], + "v3.2.0": ["v3.2.0.zip", "v3.2.0.tar.gz"], + "v3.3.0": ["v3.3.0.zip", "v3.3.0.tar.gz"], + "v4.0.0": [ + "casanovo_massivekb.ckpt", + "casanovo_nontryptic.ckpt", + "v4.0.0.zip", + "v4.0.0.tar.gz", + ], + }, + ): + self.releases = [ + MockRelease(tag_name, assets) + for tag_name, assets in release_dict.items() + ] + + def get_releases(self): + return self.releases + + +class MockGithub: + def __init__(self, releases): + self.releases = releases + + def get_repo(self, repo_name): + return MockRepo() + + +def test_setup_model(monkeypatch): + test_releases = ["3.0.0", "3.0.999", "3.999.999"] + mock_get = MockResponseGet() + mock_github = functools.partial(MockGithub, test_releases) + version = "3.0.0" + + # Test model is none when not training + with monkeypatch.context() as mnk, tempfile.TemporaryDirectory() as tmp_dir: + mnk.setattr(casanovo, "__version__", version) + mnk.setattr("appdirs.user_cache_dir", lambda n, a, opinion: tmp_dir) + mnk.setattr(github, "Github", mock_github) + mnk.setattr(requests, "get", mock_get) + filename = pathlib.Path(tmp_dir) / "casanovo_massivekb_v3_0_0.ckpt" + + assert not filename.is_file() + _, result_path = casanovo.setup_model(None, None, None, False) + assert result_path.resolve() == filename.resolve() + assert filename.is_file() + assert mock_get.request_counter == 1 + os.remove(result_path) + + assert not filename.is_file() + _, result = casanovo.setup_model(None, None, None, True) + assert result is None + assert not filename.is_file() + assert mock_get.request_counter == 1 + + with monkeypatch.context() as mnk, tempfile.TemporaryDirectory() as tmp_dir: + mnk.setattr(casanovo, "__version__", version) + mnk.setattr("appdirs.user_cache_dir", lambda n, a, opinion: tmp_dir) + mnk.setattr(github, "Github", mock_github) + mnk.setattr(requests, "get", mock_get) + + cache_file_name = "model_weights.ckpt" + file_url = f"http://www.example.com/{cache_file_name}" + url_hash = hashlib.shake_256(file_url.encode("utf-8")).hexdigest(5) + cache_dir = pathlib.Path(tmp_dir) + cache_file_dir = cache_dir / url_hash + cache_file_path = cache_file_dir / cache_file_name + + assert not cache_file_path.is_file() + _, result_path = casanovo.setup_model(file_url, None, None, False) + assert cache_file_path.is_file() + assert result_path.resolve() == cache_file_path.resolve() + assert mock_get.request_counter == 2 + os.remove(result_path) + + assert not cache_file_path.is_file() + _, result_path = casanovo.setup_model(file_url, None, None, False) + assert cache_file_path.is_file() + assert result_path.resolve() == cache_file_path.resolve() + assert mock_get.request_counter == 3 + + # Test model is file + with monkeypatch.context() as mnk, tempfile.NamedTemporaryFile( + suffix=".ckpt" + ) as temp_file, tempfile.TemporaryDirectory() as tmp_dir: + mnk.setattr(casanovo, "__version__", version) + mnk.setattr("appdirs.user_cache_dir", lambda n, a, opinion: tmp_dir) + mnk.setattr(github, "Github", mock_github) + mnk.setattr(requests, "get", mock_get) + + temp_file_path = temp_file.name + _, result = casanovo.setup_model(temp_file_path, None, None, False) + assert mock_get.request_counter == 3 + assert result == temp_file_path + + _, result = casanovo.setup_model(temp_file_path, None, None, True) + assert mock_get.request_counter == 3 + assert result == temp_file_path + + # Test model is neither a URL or File + with monkeypatch.context() as mnk, tempfile.TemporaryDirectory() as tmp_dir: + mnk.setattr(casanovo, "__version__", version) + mnk.setattr("appdirs.user_cache_dir", lambda n, a, opinion: tmp_dir) + mnk.setattr(github, "Github", mock_github) + mnk.setattr(requests, "get", mock_get) + + with pytest.raises(ValueError): + casanovo.setup_model("FooBar", None, None, False) + + assert mock_get.request_counter == 3 + + with pytest.raises(ValueError): + casanovo.setup_model("FooBar", None, None, False) + + assert mock_get.request_counter == 3 + + def test_get_model_weights(monkeypatch): """ Test that model weights can be downloaded from GitHub or used from the @@ -77,26 +250,37 @@ def test_get_model_weights(monkeypatch): """ # Model weights for fully matching version, minor matching version, major # matching version. - for version in ["3.0.0", "3.0.999", "3.999.999"]: + test_releases = ["3.0.0", "3.0.999", "3.999.999"] + mock_get = MockResponseGet() + mock_github = functools.partial(MockGithub, test_releases) + + for version in test_releases: with monkeypatch.context() as mnk, tempfile.TemporaryDirectory() as tmp_dir: mnk.setattr(casanovo, "__version__", version) mnk.setattr( "appdirs.user_cache_dir", lambda n, a, opinion: tmp_dir ) - - filename = os.path.join(tmp_dir, "casanovo_massivekb_v3_0_0.ckpt") - assert not os.path.isfile(filename) - assert casanovo._get_model_weights() == filename - assert os.path.isfile(filename) - assert casanovo._get_model_weights() == filename + mnk.setattr(github, "Github", mock_github) + mnk.setattr(requests, "get", mock_get) + + tmp_path = pathlib.Path(tmp_dir) + filename = tmp_path / "casanovo_massivekb_v3_0_0.ckpt" + assert not filename.is_file() + result_path = casanovo._get_model_weights(tmp_path) + assert result_path == filename + assert filename.is_file() + result_path = casanovo._get_model_weights(tmp_path) + assert result_path == filename # Impossible to find model weights for (i) full version mismatch and (ii) # major version mismatch. for version in ["999.999.999", "999.0.0"]: - with monkeypatch.context() as mnk: + with monkeypatch.context() as mnk, tempfile.TemporaryDirectory() as tmp_dir: mnk.setattr(casanovo, "__version__", version) + mnk.setattr(github, "Github", mock_github) + mnk.setattr(requests, "get", mock_get) with pytest.raises(ValueError): - casanovo._get_model_weights() + casanovo._get_model_weights(pathlib.Path(tmp_dir)) # Test GitHub API rate limit. def request(self, *args, **kwargs): @@ -107,8 +291,122 @@ def request(self, *args, **kwargs): with monkeypatch.context() as mnk, tempfile.TemporaryDirectory() as tmp_dir: mnk.setattr("appdirs.user_cache_dir", lambda n, a, opinion: tmp_dir) mnk.setattr("github.Requester.Requester.requestJsonAndCheck", request) + mnk.setattr(requests, "get", mock_get) + mock_get.request_counter = 0 with pytest.raises(github.RateLimitExceededException): - casanovo._get_model_weights() + casanovo._get_model_weights(pathlib.Path(tmp_dir)) + + assert mock_get.request_counter == 0 + + +class MockResponseHead: + def __init__(self): + self.last_modified = None + self.is_ok = True + self.fail = False + + def __call__(self, url): + if self.fail: + raise requests.ConnectionError + + response = unittest.mock.MagicMock() + response.headers = dict() + response.ok = self.is_ok + if self.last_modified is not None: + response.headers["Last-Modified"] = self.last_modified + + return response + + +def test_get_weights_from_url(monkeypatch): + file_url = "http://example.com/model_weights.ckpt" + + with monkeypatch.context() as mnk, tempfile.TemporaryDirectory() as tmp_dir: + mock_get = MockResponseGet() + mock_head = MockResponseHead() + mnk.setattr(requests, "get", mock_get) + mnk.setattr(requests, "head", mock_head) + + cache_dir = pathlib.Path(tmp_dir) + url_hash = hashlib.shake_256(file_url.encode("utf-8")).hexdigest(5) + cache_file_name = "model_weights.ckpt" + cache_file_dir = cache_dir / url_hash + cache_file_path = cache_file_dir / cache_file_name + + # Test downloading and caching the file + assert not cache_file_path.is_file() + result_path = casanovo._get_weights_from_url(file_url, cache_dir) + assert cache_file_path.is_file() + assert result_path.resolve() == cache_file_path.resolve() + assert mock_get.request_counter == 1 + + # Test that cached file is used + result_path = casanovo._get_weights_from_url(file_url, cache_dir) + assert result_path.resolve() == cache_file_path.resolve() + assert mock_get.request_counter == 1 + + # Test force downloading the file + result_path = casanovo._get_weights_from_url( + file_url, cache_dir, force_download=True + ) + assert result_path.resolve() == cache_file_path.resolve() + assert mock_get.request_counter == 2 + + # Test that file is re-downloaded if last modified is newer than + # file last modified + # NOTE: Assuming test takes < 1 year to run + curr_utc = datetime.datetime.now().astimezone(datetime.timezone.utc) + mock_head.last_modified = ( + curr_utc + datetime.timedelta(days=365.0) + ).strftime("%a, %d %b %Y %H:%M:%S GMT") + result_path = casanovo._get_weights_from_url(file_url, cache_dir) + assert result_path.resolve() == cache_file_path.resolve() + assert mock_get.request_counter == 3 + + # Test file is not redownloaded if its newer than upstream file + mock_head.last_modified = ( + curr_utc - datetime.timedelta(days=365.0) + ).strftime("%a, %d %b %Y %H:%M:%S GMT") + result_path = casanovo._get_weights_from_url(file_url, cache_dir) + assert result_path.resolve() == cache_file_path.resolve() + assert mock_get.request_counter == 3 + + # Test that error is raised if file get response is not OK + mock_get.is_ok = False + with pytest.raises(requests.HTTPError): + casanovo._get_weights_from_url( + file_url, cache_dir, force_download=True + ) + mock_get.is_ok = True + assert mock_get.request_counter == 4 + + # Test that cached file is used if head requests yields non-ok status + # code, even if upstream file is newer + mock_head.is_ok = False + mock_head.last_modified = ( + curr_utc + datetime.timedelta(days=365.0) + ).strftime("%a, %d %b %Y %H:%M:%S GMT") + result_path = casanovo._get_weights_from_url(file_url, cache_dir) + assert result_path.resolve() == cache_file_path.resolve() + assert mock_get.request_counter == 4 + mock_head.is_ok = True + + # Test that cached file is used if head request fails + mock_head.fail = True + result_path = casanovo._get_weights_from_url(file_url, cache_dir) + assert result_path.resolve() == cache_file_path.resolve() + assert mock_get.request_counter == 4 + mock_head.fail = False + + # Test invalid URL + with pytest.raises(ValueError): + bad_url = "foobar" + casanovo._get_weights_from_url(bad_url, cache_dir) + + +def test_is_valid_url(): + assert casanovo._is_valid_url("https://www.washington.edu/") + assert not casanovo._is_valid_url("foobar") def test_tensorboard(): @@ -597,11 +895,10 @@ def test_train_val_step_functions(): spectra = torch.zeros(1, 5, 2) precursors = torch.tensor([[469.25364, 2.0, 235.63410]]) peptides = ["PEPK"] - spectrum_id = "foobar" - batch = (spectra, precursors, spectrum_id, peptides) + batch = (spectra, precursors, peptides) train_step_loss = model.training_step(batch) - val_step_loss, _ = model.validation_step(batch) + val_step_loss = model.validation_step(batch) # Check if valid loss value returned assert train_step_loss > 0 From 0862a7cd4dcb822a0a33d6d30caf6cf096e3ac6f Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 6 Aug 2024 14:22:23 -0700 Subject: [PATCH 11/36] CLI documentation --- casanovo/casanovo.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index 98597162..48ed7c79 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -133,7 +133,12 @@ def main() -> None: "-e", is_flag=True, default=False, - help="Run in evaluation mode.", + help=""" + Run in evaluation mode. When this flag is set the peptide and amino + acid precision will be calculate and logged at the end of the sequencing + run. All input files must be annotated MGF files if running in evaluation + mode. + """, ) def sequence( peak_path: Tuple[str], @@ -146,7 +151,8 @@ def sequence( """De novo sequence peptides from tandem mass spectra. PEAK_PATH must be one or more mzML, mzXML, or MGF files from which - to sequence peptides. + to sequence peptides. If evaluate is set to true peak_path must be + one or more annotated MGF file. """ output = setup_logging(output, verbosity) config, model = setup_model(model, config, output, False) From 8461608c1a435c401c1fd4748f05fb624532adca Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 6 Aug 2024 21:25:05 +0000 Subject: [PATCH 12/36] Generate new screengrabs with rich-codex --- docs/images/evaluate-help.svg | 143 ++++++-------------------- docs/images/help.svg | 159 +++++++++++++++++++++++++++-- docs/images/sequence-help.svg | 182 ++++++++++++++++++++-------------- 3 files changed, 289 insertions(+), 195 deletions(-) diff --git a/docs/images/evaluate-help.svg b/docs/images/evaluate-help.svg index bd8b258f..661f0efe 100644 --- a/docs/images/evaluate-help.svg +++ b/docs/images/evaluate-help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - - $ casanovo evaluate --help - -Usage:casanovo evaluate [OPTIONS] ANNOTATED_PEAK_PATH...                       - - Evaluate de novo peptide sequencing performance.                                - ANNOTATED_PEAK_PATH must be one or more annoated MGF files, such as those       - provided by MassIVE-KB.                                                         - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*  ANNOTATED_PEAK_PATH    FILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--model-mTEXT                        Either the model weights (.ckpt │ -│                                              file) or a URL pointing to the  │ -│                                              model weights file. If not      │ -│                                              provided, Casanovo will try to  │ -│                                              download the latest release     │ -│                                              automatically.                  │ -│--output-oFILE                        The mzTab file to which results │ -│                                              will be written.                │ -│--config-cFILE                        The YAML configuration file     │ -│                                              overriding the default options. │ -│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ -│                                              logging messages. Log files are │ -│                                              always set to 'debug'.          │ -│--help-h  Show this message and exit.     │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo evaluate --help + +Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     + +Try'casanovo -h'for help +╭─ Error ──────────────────────────────────────────────────────────────────────╮ +│ No such command 'evaluate'.                                                  │ +╰──────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/help.svg b/docs/images/help.svg index baf2e237..dbdc05e0 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -1,4 +1,4 @@ - + - - + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ casanovo --help + + $ casanovo --help + +Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     + + ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  + ┃                                  Casanovo                                  ┃  + ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  + Casanovo de novo sequences peptides from tandem mass spectra using a            + Transformer model. Casanovo currently supports mzML, mzXML, and MGF files for   + de novo sequencing and annotated MGF files, such as those from MassIVE-KB, for  + training new models.                                                            + + Links:                                                                          + + • Documentation: https://casanovo.readthedocs.io                               + • Official code repository: https://github.com/Noble-Lab/casanovo              + + If you use Casanovo in your work, please cite:                                  + + • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   +mass spectrometry peptide sequencing with a transformer model. Proceedings   +of the 39th International Conference on Machine Learning - ICML '22 (2022)   +doi:10.1101/2022.02.07.479481.                                               + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--help-h    Show this message and exit.                                    │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────╮ +│configure Generate a Casanovo configuration file to customize.              │ +│sequence  De novo sequence peptides from tandem mass spectra.               │ +│train     Train a Casanovo model on your own data.                          │ +│version   Get the Casanovo version information                              │ +╰──────────────────────────────────────────────────────────────────────────────╯ + diff --git a/docs/images/sequence-help.svg b/docs/images/sequence-help.svg index 5e75dfe4..d6a015ad 100644 --- a/docs/images/sequence-help.svg +++ b/docs/images/sequence-help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - $ casanovo sequence --help - -Usage:casanovo sequence [OPTIONS] PEAK_PATH...                                 - - De novo sequence peptides from tandem mass spectra.                             - PEAK_PATH must be one or more mzMl, mzXML, or MGF files from which to sequence  - peptides.                                                                       - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*  PEAK_PATH    FILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--model-mTEXT                        Either the model weights (.ckpt │ -│                                              file) or a URL pointing to the  │ -│                                              model weights file. If not      │ -│                                              provided, Casanovo will try to  │ -│                                              download the latest release     │ -│                                              automatically.                  │ -│--output-oFILE                        The mzTab file to which results │ -│                                              will be written.                │ -│--config-cFILE                        The YAML configuration file     │ -│                                              overriding the default options. │ -│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ -│                                              logging messages. Log files are │ -│                                              always set to 'debug'.          │ -│--help-h  Show this message and exit.     │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo sequence --help + +Usage:casanovo sequence [OPTIONS] PEAK_PATH...                                 + + De novo sequence peptides from tandem mass spectra.                             + PEAK_PATH must be one or more mzML, mzXML, or MGF files from which to sequence  + peptides. If evaluate is set to true peak_path must be one or more annotated    + MGF file.                                                                       + +╭─ Arguments ──────────────────────────────────────────────────────────────────╮ +│*  PEAK_PATH    FILE[required]│ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--evaluate-e  Run in evaluation mode. When    │ +│                                              this flag is set the peptide    │ +│                                              and amino acid precision will   │ +│                                              be calculate and logged at the  │ +│                                              end of the sequencing run. All  │ +│                                              input files must be annotated   │ +│                                              MGF files if running in         │ +│                                              evaluation mode.                │ +│--model-mTEXT                        Either the model weights (.ckpt │ +│                                              file) or a URL pointing to the  │ +│                                              model weights file. If not      │ +│                                              provided, Casanovo will try to  │ +│                                              download the latest release     │ +│                                              automatically.                  │ +│--output-oFILE                        The mzTab file to which results │ +│                                              will be written.                │ +│--config-cFILE                        The YAML configuration file     │ +│                                              overriding the default options. │ +│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ +│                                              logging messages. Log files are │ +│                                              always set to 'debug'.          │ +│--help-h  Show this message and exit.     │ +╰──────────────────────────────────────────────────────────────────────────────╯ + From 148d32a147c9c77adc35413b59589217ed732fc7 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Wed, 7 Aug 2024 14:26:59 -0700 Subject: [PATCH 13/36] requested changes --- casanovo/casanovo.py | 2 +- casanovo/denovo/model_runner.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index 48ed7c79..33c3b332 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -151,7 +151,7 @@ def sequence( """De novo sequence peptides from tandem mass spectra. PEAK_PATH must be one or more mzML, mzXML, or MGF files from which - to sequence peptides. If evaluate is set to true peak_path must be + to sequence peptides. If evaluate is set to True PEAK_PATH must be one or more annotated MGF file. """ output = setup_logging(output, verbosity) diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index aed57f0c..25912a31 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -119,7 +119,7 @@ def train( ) def log_metrics(self, test_index: AnnotatedSpectrumIndex) -> None: - """Log pep_precision and aa_precision + """Log peptide precision and amino acid precision Calculate and log peptide precision and amino acid precision based off of model predictions and spectrum annotations @@ -142,8 +142,8 @@ def log_metrics(self, test_index: AnnotatedSpectrumIndex) -> None: ) ) - logger.info("Peptide Precision: %f", pep_precision) - logger.info("Amino Acid Precision: %f", aa_precision) + logger.info("Peptide Precision: %.2f%%", 100 * pep_precision) + logger.info("Amino Acid Precision: %.2f%%", 100 * aa_precision) def predict( self, peak_path: Iterable[str], output: str, evaluate: bool = False From 1981f132944190112332438aafd7bf1610cd4ae6 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 7 Aug 2024 21:29:48 +0000 Subject: [PATCH 14/36] Generate new screengrabs with rich-codex --- docs/images/help.svg | 174 --------------------------------- docs/images/sequence-help.svg | 176 +++++++++++++++++----------------- 2 files changed, 88 insertions(+), 262 deletions(-) diff --git a/docs/images/help.svg b/docs/images/help.svg index b89426d8..dbdc05e0 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -1,8 +1,4 @@ -<<<<<<< HEAD -======= - ->>>>>>> dev - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ->>>>>>> dev -<<<<<<< HEAD @@ -324,46 +190,6 @@ │version   Get the Casanovo version information                              │ ╰──────────────────────────────────────────────────────────────────────────────╯ -======= - - - - $ casanovo --help - -Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     - - ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  - ┃                                  Casanovo                                  ┃  - ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  - Casanovo de novo sequences peptides from tandem mass spectra using a            - Transformer model. Casanovo currently supports mzML, mzXML, and MGF files for   - de novo sequencing and annotated MGF files, such as those from MassIVE-KB, for  - training new models.                                                            - - Links:                                                                          - - • Documentation: https://casanovo.readthedocs.io                               - • Official code repository: https://github.com/Noble-Lab/casanovo              - - If you use Casanovo in your work, please cite:                                  - - • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   -mass spectrometry peptide sequencing with a transformer model. Proceedings   -of the 39th International Conference on Machine Learning - ICML '22 (2022)   -doi:10.1101/2022.02.07.479481.                                               - -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--help-h    Show this message and exit.                                    │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────╮ -│configure Generate a Casanovo configuration file to customize.              │ -│evaluate  Evaluate de novo peptide sequencing performance.                  │ -│sequence  De novo sequence peptides from tandem mass spectra.               │ -│train     Train a Casanovo model on your own data.                          │ -│version   Get the Casanovo version information                              │ -╰──────────────────────────────────────────────────────────────────────────────╯ - ->>>>>>> dev diff --git a/docs/images/sequence-help.svg b/docs/images/sequence-help.svg index d6a015ad..de0c9318 100644 --- a/docs/images/sequence-help.svg +++ b/docs/images/sequence-help.svg @@ -19,141 +19,141 @@ font-weight: 700; } - .terminal-3799921835-matrix { + .terminal-3925029771-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3799921835-title { + .terminal-3925029771-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3799921835-r1 { fill: #c5c8c6 } -.terminal-3799921835-r2 { fill: #d0b344 } -.terminal-3799921835-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-3799921835-r4 { fill: #68a0b3;font-weight: bold } -.terminal-3799921835-r5 { fill: #868887 } -.terminal-3799921835-r6 { fill: #cc555a } -.terminal-3799921835-r7 { fill: #d0b344;font-weight: bold } -.terminal-3799921835-r8 { fill: #8a4346 } -.terminal-3799921835-r9 { fill: #98a84b;font-weight: bold } -.terminal-3799921835-r10 { fill: #8d7b39;font-weight: bold } + .terminal-3925029771-r1 { fill: #c5c8c6 } +.terminal-3925029771-r2 { fill: #d0b344 } +.terminal-3925029771-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-3925029771-r4 { fill: #68a0b3;font-weight: bold } +.terminal-3925029771-r5 { fill: #868887 } +.terminal-3925029771-r6 { fill: #cc555a } +.terminal-3925029771-r7 { fill: #d0b344;font-weight: bold } +.terminal-3925029771-r8 { fill: #8a4346 } +.terminal-3925029771-r9 { fill: #98a84b;font-weight: bold } +.terminal-3925029771-r10 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -165,46 +165,46 @@ - + - - $ casanovo sequence --help - -Usage:casanovo sequence [OPTIONS] PEAK_PATH...                                 - - De novo sequence peptides from tandem mass spectra.                             - PEAK_PATH must be one or more mzML, mzXML, or MGF files from which to sequence  - peptides. If evaluate is set to true peak_path must be one or more annotated    - MGF file.                                                                       - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*  PEAK_PATH    FILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--evaluate-e  Run in evaluation mode. When    │ -│                                              this flag is set the peptide    │ -│                                              and amino acid precision will   │ -│                                              be calculate and logged at the  │ -│                                              end of the sequencing run. All  │ -│                                              input files must be annotated   │ -│                                              MGF files if running in         │ -│                                              evaluation mode.                │ -│--model-mTEXT                        Either the model weights (.ckpt │ -│                                              file) or a URL pointing to the  │ -│                                              model weights file. If not      │ -│                                              provided, Casanovo will try to  │ -│                                              download the latest release     │ -│                                              automatically.                  │ -│--output-oFILE                        The mzTab file to which results │ -│                                              will be written.                │ -│--config-cFILE                        The YAML configuration file     │ -│                                              overriding the default options. │ -│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ -│                                              logging messages. Log files are │ -│                                              always set to 'debug'.          │ -│--help-h  Show this message and exit.     │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo sequence --help + +Usage:casanovo sequence [OPTIONS] PEAK_PATH...                                 + + De novo sequence peptides from tandem mass spectra.                             + PEAK_PATH must be one or more mzML, mzXML, or MGF files from which to sequence  + peptides. If evaluate is set to True PEAK_PATH must be one or more annotated    + MGF file.                                                                       + +╭─ Arguments ──────────────────────────────────────────────────────────────────╮ +│*  PEAK_PATH    FILE[required]│ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--evaluate-e  Run in evaluation mode. When    │ +│                                              this flag is set the peptide    │ +│                                              and amino acid precision will   │ +│                                              be calculate and logged at the  │ +│                                              end of the sequencing run. All  │ +│                                              input files must be annotated   │ +│                                              MGF files if running in         │ +│                                              evaluation mode.                │ +│--model-mTEXT                        Either the model weights (.ckpt │ +│                                              file) or a URL pointing to the  │ +│                                              model weights file. If not      │ +│                                              provided, Casanovo will try to  │ +│                                              download the latest release     │ +│                                              automatically.                  │ +│--output-oFILE                        The mzTab file to which results │ +│                                              will be written.                │ +│--config-cFILE                        The YAML configuration file     │ +│                                              overriding the default options. │ +│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ +│                                              logging messages. Log files are │ +│                                              always set to 'debug'.          │ +│--help-h  Show this message and exit.     │ +╰──────────────────────────────────────────────────────────────────────────────╯ + From 6ffa3f8c2eb8accb5127823b93205e7a3435fafc Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Wed, 7 Aug 2024 16:07:36 -0700 Subject: [PATCH 15/36] evaluation test cases --- tests/conftest.py | 26 ++++++++++++++++++++++---- tests/unit_tests/test_runner.py | 31 +++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+), 4 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 02a6d0f2..0174957e 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -15,7 +15,15 @@ def mgf_small(tmp_path): return _create_mgf(peptides, mgf_file) -def _create_mgf(peptides, mgf_file, random_state=42): +@pytest.fixture +def mgf_small_unannotated(tmp_path): + """An MGF file with 2 unannotated spectra.""" + peptides = ["LESLIEK", "PEPTIDEK"] + mgf_file = tmp_path / "small_unannotated.mgf" + return _create_mgf(peptides, mgf_file, annotate=False) + + +def _create_mgf(peptides, mgf_file, random_state=42, annotate=True): """ Create a fake MGF file from one or more peptides. @@ -27,20 +35,25 @@ def _create_mgf(peptides, mgf_file, random_state=42): The MGF file to create. random_state : int or numpy.random.Generator, optional The random seed. The charge states are chosen to be 2 or 3 randomly. + annotate: bool, optional + Whether to add peptide annotations to mgf file Returns ------- mgf_file : Path """ rng = np.random.default_rng(random_state) - entries = [_create_mgf_entry(p, rng.choice([2, 3])) for p in peptides] + entries = [ + _create_mgf_entry(p, rng.choice([2, 3]), annotate=annotate) + for p in peptides + ] with mgf_file.open("w+") as mgf_ref: mgf_ref.write("\n".join(entries)) return mgf_file -def _create_mgf_entry(peptide, charge=2): +def _create_mgf_entry(peptide, charge=2, annotate=True): """ Create a MassIVE-KB style MGF entry for a single PSM. @@ -50,6 +63,8 @@ def _create_mgf_entry(peptide, charge=2): A peptide sequence. charge : int, optional The peptide charge state. + annotate: bool, optional + Whether to add peptide annotation to entry Returns ------- @@ -62,12 +77,15 @@ def _create_mgf_entry(peptide, charge=2): mgf = [ "BEGIN IONS", - f"SEQ={peptide}", f"PEPMASS={precursor_mz}", f"CHARGE={charge}+", f"{frags}", "END IONS", ] + + if annotate: + mgf.insert(1, f"SEQ={peptide}") + return "\n".join(mgf) diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index 6f674c64..23a95e9d 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -175,3 +175,34 @@ def test_save_final_model(tmp_path, mgf_small, tiny_config): assert model_file.exists() assert validation_file.exists() + + +def test_evaluate( + tmp_path, mgf_small, mzml_small, mgf_small_unannotated, tiny_config +): + """Test model evaluation during sequencing""" + # Train tiny model + config = Config(tiny_config) + config.max_epochs = 1 + model_file = tmp_path / "epoch=0-step=1.ckpt" + with ModelRunner(config) as runner: + runner.train([mgf_small], [mgf_small]) + + assert model_file.is_file() + + # Test evaluation with annotated peak file + result_file = tmp_path / "result.mzTab" + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mgf_small], result_file, evaluate=True) + + assert result_file.is_file() + result_file.unlink() + + # Test evaluation with unannotated peak files + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mgf_small_unannotated], result_file, evaluate=True) + + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mzml_small], result_file, evaluate=True) + + assert not result_file.is_file() From 8174ee5053efcbb6df6090a4c6d01bd658ac2a2c Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Thu, 8 Aug 2024 13:44:00 -0700 Subject: [PATCH 16/36] file warnings, evaluation tests --- casanovo/denovo/model_runner.py | 22 ++++++++++++++++++--- tests/unit_tests/test_runner.py | 35 ++++++++++++++++++++++++++++----- 2 files changed, 49 insertions(+), 8 deletions(-) diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 25912a31..1404a1fe 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -415,9 +415,15 @@ def _get_index( else: index_fname = Path(self.tmp_dir.name) / f"{uuid.uuid4().hex}.hdf5" - Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex - valid_charge = np.arange(1, self.config.max_charge + 1) - return Index(index_fname, filenames, valid_charge=valid_charge) + try: + Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex + valid_charge = np.arange(1, self.config.max_charge + 1) + return Index(index_fname, filenames, valid_charge=valid_charge) + except TypeError: + raise ValueError( + "MGF peak files must be annotated when constructing " + "annotated spectrum indices." + ) def _get_strategy(self) -> Union[str, DDPStrategy]: """Get the strategy for the Trainer. @@ -470,5 +476,15 @@ def _get_peak_filenames( for fname in glob.glob(path, recursive=True): if Path(fname).suffix.lower() in supported_ext: found_files.add(fname) + else: + warnings.warn( + f"Ignoring unsupported peak file: {fname}", RuntimeWarning + ) + + if len(found_files) == 0: + warnings.warn( + f"No supported peak files found under path(s): {list(paths)}", + RuntimeWarning, + ) return sorted(list(found_files)) diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index 23a95e9d..067ac157 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -199,10 +199,35 @@ def test_evaluate( result_file.unlink() # Test evaluation with unannotated peak files - with ModelRunner(config, model_filename=str(model_file)) as runner: - runner.predict([mgf_small_unannotated], result_file, evaluate=True) + with pytest.raises(FileNotFoundError): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mzml_small], result_file, evaluate=True) - with ModelRunner(config, model_filename=str(model_file)) as runner: - runner.predict([mzml_small], result_file, evaluate=True) + with pytest.raises(ValueError): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mgf_small_unannotated], result_file, evaluate=True) + + with pytest.raises(ValueError): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict( + [mgf_small_unannotated, mzml_small], result_file, evaluate=True + ) + + # Test mix of annotated an unannotated peak files + with pytest.warns(RuntimeWarning): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mgf_small, mzml_small], result_file, evaluate=True) - assert not result_file.is_file() + with pytest.raises(ValueError): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict( + [mgf_small, mgf_small_unannotated], result_file, evaluate=True + ) + + with pytest.raises(ValueError): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict( + [mgf_small, mgf_small_unannotated, mzml_small], + result_file, + evaluate=True, + ) From 81a3267ad7ba2ccc6ec3a93317b1f01f35fbe566 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Thu, 8 Aug 2024 15:54:35 -0700 Subject: [PATCH 17/36] fixed ubuntu specific test case bug --- tests/unit_tests/test_runner.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index 067ac157..fd52aeef 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -191,7 +191,7 @@ def test_evaluate( assert model_file.is_file() # Test evaluation with annotated peak file - result_file = tmp_path / "result.mzTab" + result_file = tmp_path / "result.mztab" with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mgf_small], result_file, evaluate=True) From 7b9557b6d6bdcf773bd3ea4d857596a68ad272e0 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Fri, 9 Aug 2024 13:30:48 -0700 Subject: [PATCH 18/36] verify annotated mgf files --- casanovo/denovo/model_runner.py | 55 +++++++++++++++++++++++++++------ tests/unit_tests/test_runner.py | 28 ++++++++++++++--- 2 files changed, 68 insertions(+), 15 deletions(-) diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 1404a1fe..b47b6688 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -8,7 +8,7 @@ import uuid import warnings from pathlib import Path -from typing import Iterable, List, Optional, Union +from typing import Iterable, List, Optional, Union, TextIO import depthcharge.masses import lightning.pytorch as pl @@ -399,6 +399,21 @@ def _get_index( msg = msg.strip() filenames = _get_peak_filenames(peak_path, ext) + if annotated: + # Filter unannotated MGF files to avoid Depth Charge exception + filtered_fnames = list() + for fname in filenames: + if Path( + fname + ).suffix.lower() == ".mgf" and not _mgf_is_annotated(fname): + warnings.warn( + f"Ignoring unannotated MGF peak file: {fname}", + RuntimeWarning, + ) + else: + filtered_fnames.append(fname) + filenames = filtered_fnames + if not filenames: not_found_err = f"Cound not find {msg} peak files" logger.error(not_found_err + " from %s", peak_path) @@ -415,15 +430,9 @@ def _get_index( else: index_fname = Path(self.tmp_dir.name) / f"{uuid.uuid4().hex}.hdf5" - try: - Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex - valid_charge = np.arange(1, self.config.max_charge + 1) - return Index(index_fname, filenames, valid_charge=valid_charge) - except TypeError: - raise ValueError( - "MGF peak files must be annotated when constructing " - "annotated spectrum indices." - ) + Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex + valid_charge = np.arange(1, self.config.max_charge + 1) + return Index(index_fname, filenames, valid_charge=valid_charge) def _get_strategy(self) -> Union[str, DDPStrategy]: """Get the strategy for the Trainer. @@ -448,6 +457,32 @@ def _get_strategy(self) -> Union[str, DDPStrategy]: return "auto" +def _mgf_is_annotated(mgf_path: TextIO) -> bool: + """Check whether MGF file is annotated + + Parameters + ---------- + mgf_path : TextIO + MGF peak file to check + + Returns + ------- + bool + Whether MGF peak file is annotated + """ + num_spectra = 0 + num_annotations = 0 + + with open(mgf_path) as f: + for curr_line in f: + if curr_line.startswith("BEGIN IONS"): + num_spectra += 1 + elif curr_line.startswith("SEQ="): + num_annotations += 1 + + return num_spectra == num_annotations + + def _get_peak_filenames( paths: Iterable[str], supported_ext: Iterable[str] ) -> List[str]: diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index fd52aeef..853e193f 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -6,7 +6,7 @@ import torch from casanovo.config import Config -from casanovo.denovo.model_runner import ModelRunner +from casanovo.denovo.model_runner import ModelRunner, _mgf_is_annotated def test_initialize_model(tmp_path, mgf_small): @@ -203,31 +203,49 @@ def test_evaluate( with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mzml_small], result_file, evaluate=True) - with pytest.raises(ValueError): + with pytest.raises(FileNotFoundError): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mgf_small_unannotated], result_file, evaluate=True) - with pytest.raises(ValueError): + with pytest.raises(FileNotFoundError): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small_unannotated, mzml_small], result_file, evaluate=True ) + # MzTab with just metadata is written in the case of FileNotFound + # early exit + result_file.unlink() + # Test mix of annotated an unannotated peak files with pytest.warns(RuntimeWarning): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mgf_small, mzml_small], result_file, evaluate=True) - with pytest.raises(ValueError): + assert result_file.is_file() + result_file.unlink() + + with pytest.warns(RuntimeWarning): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small, mgf_small_unannotated], result_file, evaluate=True ) - with pytest.raises(ValueError): + assert result_file.is_file() + result_file.unlink() + + with pytest.warns(RuntimeWarning): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small, mgf_small_unannotated, mzml_small], result_file, evaluate=True, ) + + assert result_file.is_file() + result_file.unlink() + + +def test_mgf_is_annotated(mgf_small, mgf_small_unannotated): + assert _mgf_is_annotated(mgf_small) + assert not _mgf_is_annotated(mgf_small_unannotated) From 5dd591fe7fd9d2d3a1ec789fb510352862a54cd7 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Fri, 9 Aug 2024 13:30:48 -0700 Subject: [PATCH 19/36] verify annotated mgf files --- casanovo/casanovo.py | 2 +- casanovo/denovo/model_runner.py | 55 +++++++++++++++++++++++++++------ tests/unit_tests/test_runner.py | 28 ++++++++++++++--- 3 files changed, 69 insertions(+), 16 deletions(-) diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index 33c3b332..0c220ddb 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -135,7 +135,7 @@ def main() -> None: default=False, help=""" Run in evaluation mode. When this flag is set the peptide and amino - acid precision will be calculate and logged at the end of the sequencing + acid precision will be calculated and logged at the end of the sequencing run. All input files must be annotated MGF files if running in evaluation mode. """, diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 1404a1fe..b47b6688 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -8,7 +8,7 @@ import uuid import warnings from pathlib import Path -from typing import Iterable, List, Optional, Union +from typing import Iterable, List, Optional, Union, TextIO import depthcharge.masses import lightning.pytorch as pl @@ -399,6 +399,21 @@ def _get_index( msg = msg.strip() filenames = _get_peak_filenames(peak_path, ext) + if annotated: + # Filter unannotated MGF files to avoid Depth Charge exception + filtered_fnames = list() + for fname in filenames: + if Path( + fname + ).suffix.lower() == ".mgf" and not _mgf_is_annotated(fname): + warnings.warn( + f"Ignoring unannotated MGF peak file: {fname}", + RuntimeWarning, + ) + else: + filtered_fnames.append(fname) + filenames = filtered_fnames + if not filenames: not_found_err = f"Cound not find {msg} peak files" logger.error(not_found_err + " from %s", peak_path) @@ -415,15 +430,9 @@ def _get_index( else: index_fname = Path(self.tmp_dir.name) / f"{uuid.uuid4().hex}.hdf5" - try: - Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex - valid_charge = np.arange(1, self.config.max_charge + 1) - return Index(index_fname, filenames, valid_charge=valid_charge) - except TypeError: - raise ValueError( - "MGF peak files must be annotated when constructing " - "annotated spectrum indices." - ) + Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex + valid_charge = np.arange(1, self.config.max_charge + 1) + return Index(index_fname, filenames, valid_charge=valid_charge) def _get_strategy(self) -> Union[str, DDPStrategy]: """Get the strategy for the Trainer. @@ -448,6 +457,32 @@ def _get_strategy(self) -> Union[str, DDPStrategy]: return "auto" +def _mgf_is_annotated(mgf_path: TextIO) -> bool: + """Check whether MGF file is annotated + + Parameters + ---------- + mgf_path : TextIO + MGF peak file to check + + Returns + ------- + bool + Whether MGF peak file is annotated + """ + num_spectra = 0 + num_annotations = 0 + + with open(mgf_path) as f: + for curr_line in f: + if curr_line.startswith("BEGIN IONS"): + num_spectra += 1 + elif curr_line.startswith("SEQ="): + num_annotations += 1 + + return num_spectra == num_annotations + + def _get_peak_filenames( paths: Iterable[str], supported_ext: Iterable[str] ) -> List[str]: diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index fd52aeef..853e193f 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -6,7 +6,7 @@ import torch from casanovo.config import Config -from casanovo.denovo.model_runner import ModelRunner +from casanovo.denovo.model_runner import ModelRunner, _mgf_is_annotated def test_initialize_model(tmp_path, mgf_small): @@ -203,31 +203,49 @@ def test_evaluate( with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mzml_small], result_file, evaluate=True) - with pytest.raises(ValueError): + with pytest.raises(FileNotFoundError): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mgf_small_unannotated], result_file, evaluate=True) - with pytest.raises(ValueError): + with pytest.raises(FileNotFoundError): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small_unannotated, mzml_small], result_file, evaluate=True ) + # MzTab with just metadata is written in the case of FileNotFound + # early exit + result_file.unlink() + # Test mix of annotated an unannotated peak files with pytest.warns(RuntimeWarning): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mgf_small, mzml_small], result_file, evaluate=True) - with pytest.raises(ValueError): + assert result_file.is_file() + result_file.unlink() + + with pytest.warns(RuntimeWarning): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small, mgf_small_unannotated], result_file, evaluate=True ) - with pytest.raises(ValueError): + assert result_file.is_file() + result_file.unlink() + + with pytest.warns(RuntimeWarning): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small, mgf_small_unannotated, mzml_small], result_file, evaluate=True, ) + + assert result_file.is_file() + result_file.unlink() + + +def test_mgf_is_annotated(mgf_small, mgf_small_unannotated): + assert _mgf_is_annotated(mgf_small) + assert not _mgf_is_annotated(mgf_small_unannotated) From 4b3d1a4ef69c6b71b042a82a3f8f03d2e3921abd Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 9 Aug 2024 20:38:25 +0000 Subject: [PATCH 20/36] Generate new screengrabs with rich-codex --- docs/images/sequence-help.svg | 176 +++++++++++++++++----------------- 1 file changed, 88 insertions(+), 88 deletions(-) diff --git a/docs/images/sequence-help.svg b/docs/images/sequence-help.svg index de0c9318..70570e2a 100644 --- a/docs/images/sequence-help.svg +++ b/docs/images/sequence-help.svg @@ -19,141 +19,141 @@ font-weight: 700; } - .terminal-3925029771-matrix { + .terminal-3834786767-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3925029771-title { + .terminal-3834786767-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3925029771-r1 { fill: #c5c8c6 } -.terminal-3925029771-r2 { fill: #d0b344 } -.terminal-3925029771-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-3925029771-r4 { fill: #68a0b3;font-weight: bold } -.terminal-3925029771-r5 { fill: #868887 } -.terminal-3925029771-r6 { fill: #cc555a } -.terminal-3925029771-r7 { fill: #d0b344;font-weight: bold } -.terminal-3925029771-r8 { fill: #8a4346 } -.terminal-3925029771-r9 { fill: #98a84b;font-weight: bold } -.terminal-3925029771-r10 { fill: #8d7b39;font-weight: bold } + .terminal-3834786767-r1 { fill: #c5c8c6 } +.terminal-3834786767-r2 { fill: #d0b344 } +.terminal-3834786767-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-3834786767-r4 { fill: #68a0b3;font-weight: bold } +.terminal-3834786767-r5 { fill: #868887 } +.terminal-3834786767-r6 { fill: #cc555a } +.terminal-3834786767-r7 { fill: #d0b344;font-weight: bold } +.terminal-3834786767-r8 { fill: #8a4346 } +.terminal-3834786767-r9 { fill: #98a84b;font-weight: bold } +.terminal-3834786767-r10 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -165,46 +165,46 @@ - + - - $ casanovo sequence --help - -Usage:casanovo sequence [OPTIONS] PEAK_PATH...                                 - - De novo sequence peptides from tandem mass spectra.                             - PEAK_PATH must be one or more mzML, mzXML, or MGF files from which to sequence  - peptides. If evaluate is set to True PEAK_PATH must be one or more annotated    - MGF file.                                                                       - -╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│*  PEAK_PATH    FILE[required]│ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--evaluate-e  Run in evaluation mode. When    │ -│                                              this flag is set the peptide    │ -│                                              and amino acid precision will   │ -│                                              be calculate and logged at the  │ -│                                              end of the sequencing run. All  │ -│                                              input files must be annotated   │ -│                                              MGF files if running in         │ -│                                              evaluation mode.                │ -│--model-mTEXT                        Either the model weights (.ckpt │ -│                                              file) or a URL pointing to the  │ -│                                              model weights file. If not      │ -│                                              provided, Casanovo will try to  │ -│                                              download the latest release     │ -│                                              automatically.                  │ -│--output-oFILE                        The mzTab file to which results │ -│                                              will be written.                │ -│--config-cFILE                        The YAML configuration file     │ -│                                              overriding the default options. │ -│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ -│                                              logging messages. Log files are │ -│                                              always set to 'debug'.          │ -│--help-h  Show this message and exit.     │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo sequence --help + +Usage:casanovo sequence [OPTIONS] PEAK_PATH...                                 + + De novo sequence peptides from tandem mass spectra.                             + PEAK_PATH must be one or more mzML, mzXML, or MGF files from which to sequence  + peptides. If evaluate is set to True PEAK_PATH must be one or more annotated    + MGF file.                                                                       + +╭─ Arguments ──────────────────────────────────────────────────────────────────╮ +│*  PEAK_PATH    FILE[required]│ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--evaluate-e  Run in evaluation mode. When    │ +│                                              this flag is set the peptide    │ +│                                              and amino acid precision will   │ +│                                              be calculated and logged at the │ +│                                              end of the sequencing run. All  │ +│                                              input files must be annotated   │ +│                                              MGF files if running in         │ +│                                              evaluation mode.                │ +│--model-mTEXT                        Either the model weights (.ckpt │ +│                                              file) or a URL pointing to the  │ +│                                              model weights file. If not      │ +│                                              provided, Casanovo will try to  │ +│                                              download the latest release     │ +│                                              automatically.                  │ +│--output-oFILE                        The mzTab file to which results │ +│                                              will be written.                │ +│--config-cFILE                        The YAML configuration file     │ +│                                              overriding the default options. │ +│--verbosity-v[debug|info|warning|error]  Set the verbosity of console    │ +│                                              logging messages. Log files are │ +│                                              always set to 'debug'.          │ +│--help-h  Show this message and exit.     │ +╰──────────────────────────────────────────────────────────────────────────────╯ + From ba58668171d4ea29796df1dfe771c52fd2ca34a1 Mon Sep 17 00:00:00 2001 From: Gwenneth Straub Date: Mon, 12 Aug 2024 10:10:30 -0700 Subject: [PATCH 21/36] Save best model (#365) * save best model * save best model * updated unit tests * remove save top k config item * added save_top_k to deprecated config options * changelog entry * test case, formatting * requested changes --- CHANGELOG.md | 4 ++++ casanovo/config.py | 22 +++++++++++++++------- casanovo/config.yaml | 3 --- casanovo/denovo/model_runner.py | 24 +++++++++++++----------- tests/conftest.py | 1 - tests/test_integration.py | 2 ++ tests/unit_tests/test_config.py | 11 ++++++++++- tests/unit_tests/test_runner.py | 4 ++-- 8 files changed, 46 insertions(+), 25 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9bd936a4..c4559d33 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Precursor charges are exported as integers instead of floats in the mzTab output file, in compliance with the mzTab specification. +### Removed + +- Removed the `save_top_k` option from the Casanovo config, the model with the lowest validation loss during training will now be saved to a fixed filename `.best.ckpt`. + ## [4.2.1] - 2024-06-25 ### Fixed diff --git a/casanovo/config.py b/casanovo/config.py index 792da35a..453f7b15 100644 --- a/casanovo/config.py +++ b/casanovo/config.py @@ -18,6 +18,7 @@ _config_deprecated = dict( every_n_train_steps="val_check_interval", max_iters="cosine_schedule_period_iters", + save_top_k=None, ) @@ -74,7 +75,6 @@ class Config: top_match=int, max_epochs=int, num_sanity_val_steps=int, - save_top_k=int, model_save_folder_path=str, val_check_interval=int, calculate_precision=bool, @@ -96,12 +96,20 @@ def __init__(self, config_file: Optional[str] = None): # Remap deprecated config entries. for old, new in _config_deprecated.items(): if old in self._user_config: - self._user_config[new] = self._user_config.pop(old) - warnings.warn( - f"Deprecated config option '{old}' remapped to " - f"'{new}'", - DeprecationWarning, - ) + if new is not None: + self._user_config[new] = self._user_config.pop(old) + warning_msg = ( + f"Deprecated config option '{old}' " + f"remapped to '{new}'" + ) + else: + del self._user_config[old] + warning_msg = ( + f"Deprecated config option '{old}' " + "is no longer in use" + ) + + warnings.warn(warning_msg, DeprecationWarning) # Check for missing entries in config file. config_missing = self._params.keys() - self._user_config.keys() if len(config_missing) > 0: diff --git a/casanovo/config.yaml b/casanovo/config.yaml index c7186ff7..3beb5f30 100644 --- a/casanovo/config.yaml +++ b/casanovo/config.yaml @@ -42,9 +42,6 @@ random_seed: 454 n_log: 1 # Tensorboard directory to use for keeping track of training metrics. tb_summarywriter: -# Save the top k model checkpoints during training. -1 saves all, and leaving -# this field empty saves none. -save_top_k: 5 # Path to saved checkpoints. model_save_folder_path: "" # Model validation and checkpointing frequency in training steps. diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index d5acacb3..07ec4166 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -36,12 +36,15 @@ class ModelRunner: model_filename : str, optional The model filename is required for eval and de novo modes, but not for training a model from scratch. + output_rootname : str, optional + The rootname for all output files (e.g. checkpoints or results) """ def __init__( self, config: Config, model_filename: Optional[str] = None, + output_rootname: Optional[str] = None, ) -> None: """Initialize a ModelRunner""" self.config = config @@ -54,24 +57,23 @@ def __init__( self.loaders = None self.writer = None + best_filename = "best" + if output_rootname is not None: + best_filename = f"{output_rootname}.{best_filename}" + # Configure checkpoints. self.callbacks = [ ModelCheckpoint( dirpath=config.model_save_folder_path, save_on_train_epoch_end=True, - ) + ), + ModelCheckpoint( + dirpath=config.model_save_folder_path, + monitor="valid_CELoss", + filename=best_filename, + ), ] - if config.save_top_k is not None: - self.callbacks.append( - ModelCheckpoint( - dirpath=config.model_save_folder_path, - monitor="valid_CELoss", - mode="min", - save_top_k=config.save_top_k, - ) - ) - def __enter__(self): """Enter the context manager""" self.tmp_dir = tempfile.TemporaryDirectory() diff --git a/tests/conftest.py b/tests/conftest.py index 02a6d0f2..54c8d03c 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -208,7 +208,6 @@ def tiny_config(tmp_path): "random_seed": 454, "n_log": 1, "tb_summarywriter": None, - "save_top_k": 5, "n_peaks": 150, "min_mz": 50.0, "max_mz": 2500.0, diff --git a/tests/test_integration.py b/tests/test_integration.py index a622b188..3c6718f5 100644 --- a/tests/test_integration.py +++ b/tests/test_integration.py @@ -36,8 +36,10 @@ def test_train_and_run( result = run(train_args) model_file = tmp_path / "epoch=19-step=20.ckpt" + best_model = tmp_path / "best.ckpt" assert result.exit_code == 0 assert model_file.exists() + assert best_model.exists() # Try evaluating: eval_args = [ diff --git a/tests/unit_tests/test_config.py b/tests/unit_tests/test_config.py index fbe10eee..14d2abe5 100644 --- a/tests/unit_tests/test_config.py +++ b/tests/unit_tests/test_config.py @@ -43,9 +43,18 @@ def test_deprecated(tmp_path, tiny_config): filename = str(tmp_path / "config_deprecated.yml") with open(tiny_config, "r") as f_in, open(filename, "w") as f_out: cfg = yaml.safe_load(f_in) - # Insert deprecated config option. + # Insert remapped deprecated config option. cfg["max_iters"] = 1 yaml.safe_dump(cfg, f_out) with pytest.warns(DeprecationWarning): Config(filename) + + with open(tiny_config, "r") as f_in, open(filename, "w") as f_out: + cfg = yaml.safe_load(f_in) + # Insert non-remapped deprecated config option. + cfg["save_top_k"] = 5 + yaml.safe_dump(cfg, f_out) + + with pytest.warns(DeprecationWarning): + Config(filename) diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index 2d0513bd..b39c3758 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -168,8 +168,8 @@ def test_save_final_model(tmp_path, mgf_small, tiny_config): # Test checkpoint saving when val_check_interval is not a factor of training steps config.val_check_interval = 15 - validation_file = tmp_path / "epoch=14-step=15.ckpt" - with ModelRunner(config) as runner: + validation_file = tmp_path / "foobar.best.ckpt" + with ModelRunner(config, output_rootname="foobar") as runner: runner.train([mgf_small], [mgf_small]) assert model_file.exists() From bd8ceba107ba6892e988b2ffbc04c6a20865c87a Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 30 Jul 2024 15:03:27 -0700 Subject: [PATCH 22/36] prediction output in model eval mode --- bar.mztab | 189 ++++++++++++++++++++++++++++++++ casanovo/data/datasets.py | 10 +- casanovo/denovo/dataloaders.py | 8 +- casanovo/denovo/model.py | 72 +++++++++--- casanovo/denovo/model_runner.py | 10 +- foo.mztab | 189 ++++++++++++++++++++++++++++++++ 6 files changed, 460 insertions(+), 18 deletions(-) create mode 100644 bar.mztab create mode 100644 foo.mztab diff --git a/bar.mztab b/bar.mztab new file mode 100644 index 00000000..cbcd1bb5 --- /dev/null +++ b/bar.mztab @@ -0,0 +1,189 @@ +MTD mzTab-version 1.0.0 +MTD mzTab-mode Summary +MTD mzTab-type Identification +MTD description Casanovo identification file bar +MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] +MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] +MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] +MTD fixed_mod[1]-site C +MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[1]-site N +MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[2]-site Q +MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] +MTD variable_mod[3]-site M +MTD variable_mod[4] [UNIMOD, UNIMOD:5, Carbamyl, ] +MTD variable_mod[4]-site N-term +MTD variable_mod[5] [UNIMOD, UNIMOD:385, Ammonia-loss, ] +MTD variable_mod[5]-site N-term +MTD variable_mod[6] [UNIMOD, UNIMOD:1, Acetyl, ] +MTD variable_mod[6]-site N-term +MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt +MTD software[1]-setting[2] config_filename = default +MTD software[1]-setting[3] precursor_mass_tol = 50.0 +MTD software[1]-setting[4] isotope_error_range = (0, 1) +MTD software[1]-setting[5] min_peptide_len = 6 +MTD software[1]-setting[6] predict_batch_size = 1024 +MTD software[1]-setting[7] n_beams = 1 +MTD software[1]-setting[8] top_match = 1 +MTD software[1]-setting[9] accelerator = auto +MTD software[1]-setting[10] devices = None +MTD software[1]-setting[11] random_seed = 454 +MTD software[1]-setting[12] n_log = 1 +MTD software[1]-setting[13] tb_summarywriter = None +MTD software[1]-setting[14] save_top_k = 5 +MTD software[1]-setting[15] model_save_folder_path = +MTD software[1]-setting[16] val_check_interval = 50000 +MTD software[1]-setting[17] n_peaks = 150 +MTD software[1]-setting[18] min_mz = 50.0 +MTD software[1]-setting[19] max_mz = 2500.0 +MTD software[1]-setting[20] min_intensity = 0.01 +MTD software[1]-setting[21] remove_precursor_tol = 2.0 +MTD software[1]-setting[22] max_charge = 10 +MTD software[1]-setting[23] dim_model = 512 +MTD software[1]-setting[24] n_head = 8 +MTD software[1]-setting[25] dim_feedforward = 1024 +MTD software[1]-setting[26] n_layers = 9 +MTD software[1]-setting[27] dropout = 0.0 +MTD software[1]-setting[28] dim_intensity = None +MTD software[1]-setting[29] max_length = 100 +MTD software[1]-setting[30] warmup_iters = 100000 +MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 +MTD software[1]-setting[32] learning_rate = 0.0005 +MTD software[1]-setting[33] weight_decay = 1e-05 +MTD software[1]-setting[34] train_label_smoothing = 0.01 +MTD software[1]-setting[35] train_batch_size = 32 +MTD software[1]-setting[36] max_epochs = 30 +MTD software[1]-setting[37] num_sanity_val_steps = 0 +MTD software[1]-setting[38] calculate_precision = False +MTD software[1]-setting[40] n_workers = 0 +MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf +PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores +PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 +PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 +PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 +PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 +PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 +PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 +PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 +PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 +PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 +PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 +PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 +PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 +PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 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null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879539277818468 null null 2 441.73788 441.73761731688 ms_run[1]:index=27 null null null null 0.98716,0.98573,0.98970,0.98983,0.98921,0.98323,0.98926,0.98847 +PSM LQHEATAATQK 29 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9673882275819778 null null 2 599.3142 599.31474381688 ms_run[1]:index=28 null null null null 0.97810,0.97690,0.97761,0.96875,0.88905,0.98107,0.97901,0.94171,0.98001,0.97853,0.97914 +PSM KEAPAPPK 30 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.99110433128145 null null 2 419.24496 419.24507831688004 ms_run[1]:index=29 null null null null 0.98966,0.99341,0.99059,0.99097,0.99120,0.99191,0.99078,0.99143 +PSM ERDELR 31 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9874146069799151 null null 2 409.2106 409.2117663168801 ms_run[1]:index=30 null null null null 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MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9210587590932846 null null 2 846.8801 846.88156881688 ms_run[1]:index=48 null null null null 0.94103,0.95696,0.85467,0.95359,0.83247,0.95710,0.95140,0.93730,0.90773,0.95238,0.95063,0.87036,0.95098,0.81020,0.95436 +PSM NKPGVYTK 50 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9890277054574754 null null 2 453.75558 453.75580581688007 ms_run[1]:index=49 null null null null 0.98844,0.98980,0.99009,0.98958,0.98979,0.98914,0.98524,0.98951 +PSM RPHETGPK 51 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.2289043515920639 null null 2 458.71735 461.2486793168801 ms_run[1]:index=50 null null null null 0.75371,0.81041,0.48279,0.64929,0.75662,0.86533,0.86147,0.87961 +PSM NHGEEHC+57.021AEHK 52 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6672931350767612 null null 2 674.28986 674.2783748168799 ms_run[1]:index=51 null null null null 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ms_run[1]:index=105 null null null null 0.42189,0.79374,0.76732,0.44555,0.50619,0.52009,0.46332,0.59417,0.82448,0.66210,0.82893,0.82902,0.82790 +PSM NVHELEK 107 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9881609752774239 null null 2 434.7295 434.72979181688004 ms_run[1]:index=106 null null null null 0.98844,0.98742,0.98892,0.98666,0.98955,0.98984,0.98553 +PSM YPNHSVDR 108 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9701713191138374 null null 2 494.2362 494.23577281688 ms_run[1]:index=107 null null null null 0.98136,0.88748,0.97896,0.98037,0.98181,0.97936,0.98056,0.98167 +PSM NKEGEVDYAK 109 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8123747543855147 null null 2 576.78033 576.7802103168799 ms_run[1]:index=108 null null null null 0.90083,0.90001,0.89895,0.59818,0.57671,0.56759,0.90301,0.89488,0.90020,0.89448 +PSM LRPEPNTGK 110 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.052142149209976174 null null 2 499.27567 506.28271881688005 ms_run[1]:index=109 null null null null 0.96482,0.96376,0.96742,0.96250,0.96909,0.84115,0.96040,0.94795,0.93244 +PSM NN+0.984EELNK 111 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20876559987664223 null null 2 421.71188 431.20106381688004 ms_run[1]:index=110 null null null null 0.89154,0.89164,0.89013,0.88795,0.88142,0.61297,0.87860 +PSM PHESNYEEDGK 112 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3362173897524675 null null 2 646.7648 652.77311331688 ms_run[1]:index=111 null null null null 0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 +PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 +PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 +PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 +PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 +PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 +PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 +PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 +PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 +PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 +PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 +PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 +PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 +PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 +PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 +PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 +PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 diff --git a/casanovo/data/datasets.py b/casanovo/data/datasets.py index 6244e88f..f7b2fe7e 100644 --- a/casanovo/data/datasets.py +++ b/casanovo/data/datasets.py @@ -87,6 +87,7 @@ def __getitem__( spectrum = self._process_peaks( mz_array, int_array, precursor_mz, precursor_charge ) + return ( spectrum, precursor_mz, @@ -264,4 +265,11 @@ def __getitem__(self, idx: int) -> Tuple[torch.Tensor, float, int, str]: spectrum = self._process_peaks( mz_array, int_array, precursor_mz, precursor_charge ) - return spectrum, precursor_mz, precursor_charge, peptide + + return ( + spectrum, + precursor_mz, + precursor_charge, + self.get_spectrum_id(idx), + peptide, + ) diff --git a/casanovo/denovo/dataloaders.py b/casanovo/denovo/dataloaders.py index fe5d6237..ba58d83c 100644 --- a/casanovo/denovo/dataloaders.py +++ b/casanovo/denovo/dataloaders.py @@ -202,7 +202,11 @@ def prepare_batch( The spectrum identifiers (during de novo sequencing) or peptide sequences (during training). """ - spectra, precursor_mzs, precursor_charges, spectrum_ids = list(zip(*batch)) + batch_list = list(zip(*batch)) + spectra, precursor_mzs, precursor_charges, spectrum_ids = batch_list[0:4] + peptide_sequence = ( + None if len(batch_list) <= 4 else np.asarray(batch_list[4]) + ) spectra = torch.nn.utils.rnn.pad_sequence(spectra, batch_first=True) precursor_mzs = torch.tensor(precursor_mzs) precursor_charges = torch.tensor(precursor_charges) @@ -210,4 +214,4 @@ def prepare_batch( precursors = torch.vstack( [precursor_masses, precursor_charges, precursor_mzs] ).T.float() - return spectra, precursors, np.asarray(spectrum_ids) + return spectra, precursors, np.asarray(spectrum_ids), peptide_sequence diff --git a/casanovo/denovo/model.py b/casanovo/denovo/model.py index 77df6df5..29acaf40 100644 --- a/casanovo/denovo/model.py +++ b/casanovo/denovo/model.py @@ -748,7 +748,7 @@ def training_step( torch.Tensor The loss of the training step. """ - pred, truth = self._forward_step(*batch) + pred, truth = self._forward_step(batch[0], batch[1], batch[3]) pred = pred[:, :-1, :].reshape(-1, self.decoder.vocab_size + 1) if mode == "train": loss = self.celoss(pred, truth.flatten()) @@ -781,14 +781,15 @@ def validation_step( The loss of the validation step. """ # Record the loss. + forward_step = self.forward(batch[0], batch[1]) loss = self.training_step(batch, mode="valid") if not self.calculate_precision: - return loss + return loss, self._get_predictions(batch, forward_step) # Calculate and log amino acid and peptide match evaluation metrics from # the predicted peptides. peptides_pred, peptides_true = [], batch[2] - for spectrum_preds in self.forward(batch[0], batch[1]): + for spectrum_preds in forward_step: for _, _, pred in spectrum_preds: peptides_pred.append(pred) @@ -810,26 +811,35 @@ def validation_step( aa_precision, **log_args, ) - return loss + return loss, self._get_predictions(batch, forward_step) - def predict_step( - self, batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], *args + def _get_predictions( + self, + batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], + forward_res: List[List[Tuple[float, np.ndarray, str]]], ) -> List[Tuple[np.ndarray, float, float, str, float, np.ndarray]]: """ - A single prediction step. + Extract predictions from model output for a batch of spectra. + + Processes the output from a forward pass of the model to + generate a list of predictions for each spectrum in the batch. Parameters ---------- batch : Tuple[torch.Tensor, torch.Tensor, torch.Tensor] - A batch of (i) MS/MS spectra, (ii) precursor information, (iii) - spectrum identifiers as torch Tensors. + A tuple containing: + - (i) MS/MS spectra data as a torch.Tensor. + - (ii) Precursor information, including charge and m/z values, + - (iii) Spectrum identifiers as a torch.Tensor. + forward_res : List[List[Tuple[float, np.ndarray, str]]] + Output from forward_step Returns ------- - predictions: List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] - Model predictions for the given batch of spectra containing spectrum - ids, precursor information, peptide sequences as well as peptide - and amino acid-level confidence scores. + List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] + Model predictions for the given batch of spectra containing + spectrum ids, precursor information, peptide sequences as well as + peptide and amino acid-level confidence scores. """ predictions = [] for ( @@ -841,7 +851,7 @@ def predict_step( batch[1][:, 1].cpu().detach().numpy(), batch[1][:, 2].cpu().detach().numpy(), batch[2], - self.forward(batch[0], batch[1]), + forward_res, ): for peptide_score, aa_scores, peptide in spectrum_preds: predictions.append( @@ -857,6 +867,27 @@ def predict_step( return predictions + def predict_step( + self, batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], *args + ) -> List[Tuple[np.ndarray, float, float, str, float, np.ndarray]]: + """ + A single prediction step. + + Parameters + ---------- + batch : Tuple[torch.Tensor, torch.Tensor, torch.Tensor] + A batch of (i) MS/MS spectra, (ii) precursor information, (iii) + spectrum identifiers as torch Tensors. + + Returns + ------- + predictions: List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] + Model predictions for the given batch of spectra containing spectrum + ids, precursor information, peptide sequences as well as peptide + and amino acid-level confidence scores. + """ + return self._get_predictions(batch, self.forward(batch[0], batch[1])) + def on_train_epoch_end(self) -> None: """ Log the training loss at the end of each epoch. @@ -925,6 +956,19 @@ def on_predict_batch_end( ), ) + def on_validation_batch_end( + self, + outputs: Tuple[ + torch.Tensor, List[Tuple[np.ndarray, List[str], torch.Tensor]] + ], + *args, + ) -> None: + """ + Write the predicted peptide sequences and amino acid scores to the + output file. + """ + self.on_predict_batch_end(outputs[1]) + def _log_history(self) -> None: """ Write log to console, if requested. diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 07ec4166..19164e5d 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -130,13 +130,21 @@ def evaluate(self, peak_path: Iterable[str]) -> None: ------- self """ + self.writer = ms_io.MztabWriter(Path("foo.mztab")) + self.writer.set_metadata( + self.config, + model=str(self.model_filename), + config_filename=self.config.file, + ) + self.initialize_trainer(train=False) self.initialize_model(train=False) + self.model.out_writer = self.writer test_index = self._get_index(peak_path, True, "evaluation") + self.writer.set_ms_run(test_index.ms_files) self.initialize_data_module(test_index=test_index) self.loaders.setup(stage="test", annotated=True) - self.trainer.validate(self.model, self.loaders.test_dataloader()) def predict(self, peak_path: Iterable[str], output: str) -> None: diff --git a/foo.mztab b/foo.mztab new file mode 100644 index 00000000..aa8a6922 --- /dev/null +++ b/foo.mztab @@ -0,0 +1,189 @@ +MTD mzTab-version 1.0.0 +MTD mzTab-mode Summary +MTD mzTab-type Identification +MTD description Casanovo identification file foo +MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] +MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] +MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] +MTD fixed_mod[1]-site C +MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[1]-site N +MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[2]-site Q +MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] +MTD variable_mod[3]-site M +MTD variable_mod[4] [UNIMOD, UNIMOD:5, Carbamyl, ] +MTD variable_mod[4]-site N-term +MTD variable_mod[5] [UNIMOD, UNIMOD:1, Acetyl, ] +MTD variable_mod[5]-site N-term +MTD variable_mod[6] [UNIMOD, UNIMOD:385, Ammonia-loss, ] +MTD variable_mod[6]-site N-term +MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt +MTD software[1]-setting[2] config_filename = default +MTD software[1]-setting[3] precursor_mass_tol = 50.0 +MTD software[1]-setting[4] isotope_error_range = (0, 1) +MTD software[1]-setting[5] min_peptide_len = 6 +MTD software[1]-setting[6] predict_batch_size = 1024 +MTD software[1]-setting[7] n_beams = 1 +MTD software[1]-setting[8] top_match = 1 +MTD software[1]-setting[9] accelerator = auto +MTD software[1]-setting[10] devices = None +MTD software[1]-setting[11] random_seed = 454 +MTD software[1]-setting[12] n_log = 1 +MTD software[1]-setting[13] tb_summarywriter = None +MTD software[1]-setting[14] save_top_k = 5 +MTD software[1]-setting[15] model_save_folder_path = +MTD software[1]-setting[16] val_check_interval = 50000 +MTD software[1]-setting[17] n_peaks = 150 +MTD software[1]-setting[18] min_mz = 50.0 +MTD software[1]-setting[19] max_mz = 2500.0 +MTD software[1]-setting[20] min_intensity = 0.01 +MTD software[1]-setting[21] remove_precursor_tol = 2.0 +MTD software[1]-setting[22] max_charge = 10 +MTD software[1]-setting[23] dim_model = 512 +MTD software[1]-setting[24] n_head = 8 +MTD software[1]-setting[25] dim_feedforward = 1024 +MTD software[1]-setting[26] n_layers = 9 +MTD software[1]-setting[27] dropout = 0.0 +MTD software[1]-setting[28] dim_intensity = None +MTD software[1]-setting[29] max_length = 100 +MTD software[1]-setting[30] warmup_iters = 100000 +MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 +MTD software[1]-setting[32] learning_rate = 0.0005 +MTD software[1]-setting[33] weight_decay = 1e-05 +MTD software[1]-setting[34] train_label_smoothing = 0.01 +MTD software[1]-setting[35] train_batch_size = 32 +MTD software[1]-setting[36] max_epochs = 30 +MTD software[1]-setting[37] num_sanity_val_steps = 0 +MTD software[1]-setting[38] calculate_precision = False +MTD software[1]-setting[40] n_workers = 0 +MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf +PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores +PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 +PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 +PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 +PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 +PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 +PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 +PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 +PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 +PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 +PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 +PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 +PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 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null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9874146069799151 null null 2 409.2106 409.2117663168801 ms_run[1]:index=30 null null null null 0.98921,0.98706,0.98802,0.98241,0.98891,0.98739 +PSM EVLHANNR 32 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8818797965844473 null null 2 476.75156 476.75158981687997 ms_run[1]:index=31 null null null null 0.93772,0.73514,0.67541,0.93265,0.93705,0.93603,0.93502,0.91176 +PSM NNTLTPNKPNK 33 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1514618446429571 null null 2 613.8276 620.83584181688 ms_run[1]:index=32 null null null null 0.90068,0.80453,0.91917,0.67357,0.80102,0.91849,0.91801,0.71365,0.91622,0.90961,0.78907 +PSM MQEHMR 34 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894828966685704 null null 2 416.18372 416.18364081688 ms_run[1]:index=33 null null null null 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0.80744,0.47209,0.48691,0.43885,0.55379,0.57064,0.61858,0.83322,0.82685,0.83470,0.83499 +PSM APTQGEC+57.021HC+57.021DQTF 106 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6652015820145607 null null 2 775.8415 775.8035578168799 ms_run[1]:index=105 null null null null 0.42189,0.79374,0.76732,0.44555,0.50619,0.52009,0.46332,0.59417,0.82448,0.66210,0.82893,0.82902,0.82790 +PSM NVHELEK 107 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9881609752774239 null null 2 434.7295 434.72979181688004 ms_run[1]:index=106 null null null null 0.98844,0.98742,0.98892,0.98666,0.98955,0.98984,0.98553 +PSM YPNHSVDR 108 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9701713191138374 null null 2 494.2362 494.23577281688 ms_run[1]:index=107 null null null null 0.98136,0.88748,0.97896,0.98037,0.98181,0.97936,0.98056,0.98167 +PSM NKEGEVDYAK 109 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8123747543855147 null null 2 576.78033 576.7802103168799 ms_run[1]:index=108 null null null null 0.90083,0.90001,0.89895,0.59818,0.57671,0.56759,0.90301,0.89488,0.90020,0.89448 +PSM LRPEPNTGK 110 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.052142149209976174 null null 2 499.27567 506.28271881688005 ms_run[1]:index=109 null null null null 0.96482,0.96376,0.96742,0.96250,0.96909,0.84115,0.96040,0.94795,0.93244 +PSM NN+0.984EELNK 111 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20876559987664223 null null 2 421.71188 431.20106381688004 ms_run[1]:index=110 null null null null 0.89154,0.89164,0.89013,0.88795,0.88142,0.61297,0.87860 +PSM PHESNYEEDGK 112 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3362173897524675 null null 2 646.7648 652.77311331688 ms_run[1]:index=111 null null null null 0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 +PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 +PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 +PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 +PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 +PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 +PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 +PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 +PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 +PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 +PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 +PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 +PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 +PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 +PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 +PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 +PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 From d4326b12cdc64cd1a7195f832ca1e70648a23321 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 30 Jul 2024 15:22:11 -0700 Subject: [PATCH 23/36] eliminate eval command, introduce -e flag for predict command --- bar2.mztab | 189 ++++++++++++++++++++++++++++++++ casanovo/casanovo.py | 48 +++----- casanovo/denovo/model_runner.py | 49 +++------ foo2.mztab | 189 ++++++++++++++++++++++++++++++++ 4 files changed, 408 insertions(+), 67 deletions(-) create mode 100644 bar2.mztab create mode 100644 foo2.mztab diff --git a/bar2.mztab b/bar2.mztab new file mode 100644 index 00000000..78f5939c --- /dev/null +++ b/bar2.mztab @@ -0,0 +1,189 @@ +MTD mzTab-version 1.0.0 +MTD mzTab-mode Summary +MTD mzTab-type Identification +MTD description Casanovo identification file bar2 +MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] +MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] +MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] +MTD fixed_mod[1]-site C +MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[1]-site N +MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[2]-site Q +MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] +MTD variable_mod[3]-site M +MTD variable_mod[4] [UNIMOD, UNIMOD:385, Ammonia-loss, ] +MTD variable_mod[4]-site N-term +MTD variable_mod[5] [UNIMOD, UNIMOD:5, Carbamyl, ] +MTD variable_mod[5]-site N-term +MTD variable_mod[6] [UNIMOD, UNIMOD:1, Acetyl, ] +MTD variable_mod[6]-site N-term +MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt +MTD software[1]-setting[2] config_filename = default +MTD software[1]-setting[3] precursor_mass_tol = 50.0 +MTD software[1]-setting[4] isotope_error_range = (0, 1) +MTD software[1]-setting[5] min_peptide_len = 6 +MTD software[1]-setting[6] predict_batch_size = 1024 +MTD software[1]-setting[7] n_beams = 1 +MTD software[1]-setting[8] top_match = 1 +MTD software[1]-setting[9] accelerator = auto +MTD software[1]-setting[10] devices = None +MTD software[1]-setting[11] random_seed = 454 +MTD software[1]-setting[12] n_log = 1 +MTD software[1]-setting[13] tb_summarywriter = None +MTD software[1]-setting[14] save_top_k = 5 +MTD software[1]-setting[15] model_save_folder_path = +MTD software[1]-setting[16] val_check_interval = 50000 +MTD software[1]-setting[17] n_peaks = 150 +MTD software[1]-setting[18] min_mz = 50.0 +MTD software[1]-setting[19] max_mz = 2500.0 +MTD software[1]-setting[20] min_intensity = 0.01 +MTD software[1]-setting[21] remove_precursor_tol = 2.0 +MTD software[1]-setting[22] max_charge = 10 +MTD software[1]-setting[23] dim_model = 512 +MTD software[1]-setting[24] n_head = 8 +MTD software[1]-setting[25] dim_feedforward = 1024 +MTD software[1]-setting[26] n_layers = 9 +MTD software[1]-setting[27] dropout = 0.0 +MTD software[1]-setting[28] dim_intensity = None +MTD software[1]-setting[29] max_length = 100 +MTD software[1]-setting[30] warmup_iters = 100000 +MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 +MTD software[1]-setting[32] learning_rate = 0.0005 +MTD software[1]-setting[33] weight_decay = 1e-05 +MTD software[1]-setting[34] train_label_smoothing = 0.01 +MTD software[1]-setting[35] train_batch_size = 32 +MTD software[1]-setting[36] max_epochs = 30 +MTD software[1]-setting[37] num_sanity_val_steps = 0 +MTD software[1]-setting[38] calculate_precision = False +MTD software[1]-setting[40] n_workers = 0 +MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf +PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores +PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 +PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 +PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 +PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 +PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 +PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 +PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 +PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 +PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 +PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 +PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 +PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 +PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 +PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 +PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 +PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9672952890396118 null null 2 614.33795 614.33821831688 ms_run[1]:index=15 null null null null 0.97399,0.97959,0.97837,0.97845,0.96474,0.84979,0.97928,0.97613,0.97886,0.97760,0.97960,0.97994 +PSM LQEEERER 17 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.975036793284946 null null 2 544.77 544.77017681688 ms_run[1]:index=16 null null null null 0.91222,0.98079,0.98579,0.98252,0.98429,0.98225,0.98285,0.98220 +PSM TRGHESEMK 18 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1844959855079651 null null 2 539.25323 537.75346831688 ms_run[1]:index=17 null null null null 0.90297,0.90465,0.82135,0.90041,0.64139,0.62194,0.66087,0.89718,0.90124 +PSM +42.011KVEDPPRK 19 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.24581749439239498 null null 2 507.26154 505.78509881688007 ms_run[1]:index=18 null null null null 0.77158,0.66196,0.86775,0.87090,0.70578,0.61787,0.85217,0.69678,0.62489 +PSM TESPAEGKQEEEK 20 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.868788189121655 null null 2 731.3395 731.3388133168802 ms_run[1]:index=19 null null null null 0.92347,0.91621,0.74657,0.61987,0.87546,0.65200,0.92947,0.92629,0.93151,0.92995,0.92921,0.92534,0.92826 +PSM LVEEETKK 21 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879584113756815 null null 2 488.27112 488.27148531688005 ms_run[1]:index=20 null null null null 0.98623,0.98691,0.98852,0.98742,0.98734,0.98694,0.99077,0.98849 +PSM KAETLGEK 22 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9864536391364204 null null 2 438.24524 438.24527081688 ms_run[1]:index=21 null null null null 0.98740,0.98704,0.98770,0.98844,0.98931,0.98661,0.98774,0.97524 +PSM C+57.021LKPNETK 23 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9895809359020658 null null 2 495.25775 495.25785531688 ms_run[1]:index=22 null null null null 0.98927,0.98929,0.98595,0.99043,0.99001,0.99081,0.98784,0.99231 +PSM GHQALER 24 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9861482679843903 null null 2 405.71454 405.71447681688 ms_run[1]:index=23 null null null null 0.98369,0.97763,0.98807,0.98786,0.98838,0.98693,0.98818 +PSM TNNLRPK 25 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9859854802489281 null null 2 421.74548 421.74577181688005 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MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 +PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 +PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 +PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 +PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 +PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 +PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 +PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 +PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 +PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index cd2274a0..98597162 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -128,64 +128,44 @@ def main() -> None: nargs=-1, type=click.Path(exists=True, dir_okay=False), ) +@click.option( + "--evaluate", + "-e", + is_flag=True, + default=False, + help="Run in evaluation mode.", +) def sequence( peak_path: Tuple[str], model: Optional[str], config: Optional[str], output: Optional[str], verbosity: str, + evaluate: bool, ) -> None: """De novo sequence peptides from tandem mass spectra. - PEAK_PATH must be one or more mzMl, mzXML, or MGF files from which + PEAK_PATH must be one or more mzML, mzXML, or MGF files from which to sequence peptides. """ output = setup_logging(output, verbosity) config, model = setup_model(model, config, output, False) start_time = time.time() with ModelRunner(config, model) as runner: - logger.info("Sequencing peptides from:") + logger.info( + "Sequencing %speptides from:", + "and evaluating " if evaluate else "", + ) for peak_file in peak_path: logger.info(" %s", peak_file) - runner.predict(peak_path, output) + runner.predict(peak_path, output, evaluate=evaluate) psms = runner.writer.psms utils.log_sequencing_report( psms, start_time=start_time, end_time=time.time() ) -@main.command(cls=_SharedParams) -@click.argument( - "annotated_peak_path", - required=True, - nargs=-1, - type=click.Path(exists=True, dir_okay=False), -) -def evaluate( - annotated_peak_path: Tuple[str], - model: Optional[str], - config: Optional[str], - output: Optional[str], - verbosity: str, -) -> None: - """Evaluate de novo peptide sequencing performance. - - ANNOTATED_PEAK_PATH must be one or more annoated MGF files, - such as those provided by MassIVE-KB. - """ - output = setup_logging(output, verbosity) - config, model = setup_model(model, config, output, False) - start_time = time.time() - with ModelRunner(config, model) as runner: - logger.info("Sequencing and evaluating peptides from:") - for peak_file in annotated_peak_path: - logger.info(" %s", peak_file) - - runner.evaluate(annotated_peak_path) - utils.log_run_report(start_time=start_time, end_time=time.time()) - - @main.command(cls=_SharedParams) @click.argument( "train_peak_path", diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 19164e5d..083a0ace 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -118,36 +118,9 @@ def train( self.loaders.val_dataloader(), ) - def evaluate(self, peak_path: Iterable[str]) -> None: - """Evaluate peptide sequence preditions from a trained Casanovo model. - - Parameters - ---------- - peak_path : iterable of str - The path with MS data files for predicting peptide sequences. - - Returns - ------- - self - """ - self.writer = ms_io.MztabWriter(Path("foo.mztab")) - self.writer.set_metadata( - self.config, - model=str(self.model_filename), - config_filename=self.config.file, - ) - - self.initialize_trainer(train=False) - self.initialize_model(train=False) - self.model.out_writer = self.writer - - test_index = self._get_index(peak_path, True, "evaluation") - self.writer.set_ms_run(test_index.ms_files) - self.initialize_data_module(test_index=test_index) - self.loaders.setup(stage="test", annotated=True) - self.trainer.validate(self.model, self.loaders.test_dataloader()) - - def predict(self, peak_path: Iterable[str], output: str) -> None: + def predict( + self, peak_path: Iterable[str], output: str, evaluate=False + ) -> None: """Predict peptide sequences with a trained Casanovo model. Parameters @@ -156,6 +129,10 @@ def predict(self, peak_path: Iterable[str], output: str) -> None: The path with the MS data files for predicting peptide sequences. output : str Where should the output be saved? + evaluate: str + whether to run model evaluation in addition to inference + Note: peak_path most point to annotated MS data files when + running model evaluation Returns ------- @@ -172,11 +149,17 @@ def predict(self, peak_path: Iterable[str], output: str) -> None: self.initialize_model(train=False) self.model.out_writer = self.writer - test_index = self._get_index(peak_path, False, "") + test_index = self._get_index( + peak_path, evaluate, "evaluation" if evaluate else "" + ) self.writer.set_ms_run(test_index.ms_files) self.initialize_data_module(test_index=test_index) - self.loaders.setup(stage="test", annotated=False) - self.trainer.predict(self.model, self.loaders.test_dataloader()) + self.loaders.setup(stage="test", annotated=evaluate) + + if evaluate: + self.trainer.validate(self.model, self.loaders.test_dataloader()) + else: + self.trainer.predict(self.model, self.loaders.test_dataloader()) def initialize_trainer(self, train: bool) -> None: """Initialize the lightning Trainer. diff --git a/foo2.mztab b/foo2.mztab new file mode 100644 index 00000000..c95f7791 --- /dev/null +++ b/foo2.mztab @@ -0,0 +1,189 @@ +MTD mzTab-version 1.0.0 +MTD mzTab-mode Summary +MTD mzTab-type Identification +MTD description Casanovo identification file foo2 +MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] +MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] +MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] +MTD fixed_mod[1]-site C +MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[1]-site N +MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] +MTD variable_mod[2]-site Q +MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] +MTD variable_mod[3]-site M +MTD variable_mod[4] [UNIMOD, UNIMOD:385, Ammonia-loss, ] +MTD variable_mod[4]-site N-term +MTD variable_mod[5] [UNIMOD, UNIMOD:1, Acetyl, ] +MTD variable_mod[5]-site N-term +MTD variable_mod[6] [UNIMOD, UNIMOD:5, Carbamyl, ] +MTD variable_mod[6]-site N-term +MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt +MTD software[1]-setting[2] config_filename = default +MTD software[1]-setting[3] precursor_mass_tol = 50.0 +MTD software[1]-setting[4] isotope_error_range = (0, 1) +MTD software[1]-setting[5] min_peptide_len = 6 +MTD software[1]-setting[6] predict_batch_size = 1024 +MTD software[1]-setting[7] n_beams = 1 +MTD software[1]-setting[8] top_match = 1 +MTD software[1]-setting[9] accelerator = auto +MTD software[1]-setting[10] devices = None +MTD software[1]-setting[11] random_seed = 454 +MTD software[1]-setting[12] n_log = 1 +MTD software[1]-setting[13] tb_summarywriter = None +MTD software[1]-setting[14] save_top_k = 5 +MTD software[1]-setting[15] model_save_folder_path = +MTD software[1]-setting[16] val_check_interval = 50000 +MTD software[1]-setting[17] n_peaks = 150 +MTD software[1]-setting[18] min_mz = 50.0 +MTD software[1]-setting[19] max_mz = 2500.0 +MTD software[1]-setting[20] min_intensity = 0.01 +MTD software[1]-setting[21] remove_precursor_tol = 2.0 +MTD software[1]-setting[22] max_charge = 10 +MTD software[1]-setting[23] dim_model = 512 +MTD software[1]-setting[24] n_head = 8 +MTD software[1]-setting[25] dim_feedforward = 1024 +MTD software[1]-setting[26] n_layers = 9 +MTD software[1]-setting[27] dropout = 0.0 +MTD software[1]-setting[28] dim_intensity = None +MTD software[1]-setting[29] max_length = 100 +MTD software[1]-setting[30] warmup_iters = 100000 +MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 +MTD software[1]-setting[32] learning_rate = 0.0005 +MTD software[1]-setting[33] weight_decay = 1e-05 +MTD software[1]-setting[34] train_label_smoothing = 0.01 +MTD software[1]-setting[35] train_batch_size = 32 +MTD software[1]-setting[36] max_epochs = 30 +MTD software[1]-setting[37] num_sanity_val_steps = 0 +MTD software[1]-setting[38] calculate_precision = False +MTD software[1]-setting[40] n_workers = 0 +MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf +PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores +PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 +PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 +PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 +PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 +PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 +PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 +PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 +PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 +PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 +PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 +PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 +PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 +PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 +PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 +PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 +PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9672952890396118 null null 2 614.33795 614.33821831688 ms_run[1]:index=15 null null null null 0.97399,0.97959,0.97837,0.97845,0.96474,0.84979,0.97928,0.97613,0.97886,0.97760,0.97960,0.97994 +PSM LQEEERER 17 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.975036793284946 null null 2 544.77 544.77017681688 ms_run[1]:index=16 null null null null 0.91222,0.98079,0.98579,0.98252,0.98429,0.98225,0.98285,0.98220 +PSM TRGHESEMK 18 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1844959855079651 null null 2 539.25323 537.75346831688 ms_run[1]:index=17 null null null null 0.90297,0.90465,0.82135,0.90041,0.64139,0.62194,0.66087,0.89718,0.90124 +PSM +42.011KVEDPPRK 19 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.24581749439239498 null null 2 507.26154 505.78509881688007 ms_run[1]:index=18 null null null null 0.77158,0.66196,0.86775,0.87090,0.70578,0.61787,0.85217,0.69678,0.62489 +PSM TESPAEGKQEEEK 20 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.868788189121655 null null 2 731.3395 731.3388133168802 ms_run[1]:index=19 null null null null 0.92347,0.91621,0.74657,0.61987,0.87546,0.65200,0.92947,0.92629,0.93151,0.92995,0.92921,0.92534,0.92826 +PSM LVEEETKK 21 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879584113756815 null null 2 488.27112 488.27148531688005 ms_run[1]:index=20 null null null null 0.98623,0.98691,0.98852,0.98742,0.98734,0.98694,0.99077,0.98849 +PSM KAETLGEK 22 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9864536391364204 null null 2 438.24524 438.24527081688 ms_run[1]:index=21 null null null null 0.98740,0.98704,0.98770,0.98844,0.98931,0.98661,0.98774,0.97524 +PSM C+57.021LKPNETK 23 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9895809359020658 null null 2 495.25775 495.25785531688 ms_run[1]:index=22 null null null null 0.98927,0.98929,0.98595,0.99043,0.99001,0.99081,0.98784,0.99231 +PSM GHQALER 24 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9861482679843903 null null 2 405.71454 405.71447681688 ms_run[1]:index=23 null null null null 0.98369,0.97763,0.98807,0.98786,0.98838,0.98693,0.98818 +PSM TNNLRPK 25 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9859854802489281 null null 2 421.74548 421.74577181688005 ms_run[1]:index=24 null null null null 0.98893,0.99008,0.98974,0.98259,0.98795,0.97375,0.98633 +PSM +43.006DTPGHATPGHGAGTQER 26 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.22608531070382976 null null 2 867.40045 866.39330131688 ms_run[1]:index=25 null null null null 0.85561,0.57927,0.49126,0.50495,0.70489,0.76038,0.75372,0.53050,0.87917,0.87740,0.88139,0.87799,0.88406,0.88016,0.88217,0.87672,0.82864,0.77355 +PSM KSYTTPK 27 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8933427818119526 null null 2 412.72778 412.72925231688004 ms_run[1]:index=26 null null null null 0.93932,0.94376,0.93479,0.61684,0.94099,0.93574,0.89386 +PSM VLEGHAEK 28 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4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 +PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 +PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 +PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 +PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 +PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 +PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 +PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 From b43121e7ba4a47a577605049ebae11e8569765d1 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Wed, 31 Jul 2024 10:46:57 -0700 Subject: [PATCH 24/36] adapted unit test to new model runner and model functionality --- tests/test_integration.py | 48 ++++++++++++++++++++++----------- tests/unit_tests/test_runner.py | 7 ++--- tests/unit_tests/test_unit.py | 5 ++-- 3 files changed, 40 insertions(+), 20 deletions(-) diff --git a/tests/test_integration.py b/tests/test_integration.py index 3c6718f5..54b09741 100644 --- a/tests/test_integration.py +++ b/tests/test_integration.py @@ -41,21 +41,6 @@ def test_train_and_run( assert model_file.exists() assert best_model.exists() - # Try evaluating: - eval_args = [ - "evaluate", - "--model", - str(model_file), - "--config", - str(tiny_config), - "--output", - str(tmp_path / "eval"), - str(mgf_small), - ] - - result = run(eval_args) - assert result.exit_code == 0 - # Try predicting: output_filename = tmp_path / "test.mztab" predict_args = [ @@ -92,6 +77,39 @@ def test_train_and_run( assert psms.loc[4, "sequence"] == "PEPTLDEK" assert psms.loc[4, "spectra_ref"] == "ms_run[2]:scan=111" + # Finally, try evaluating: + output_filename = tmp_path / "test-eval.mztab" + eval_args = [ + "sequence", + "--model", + str(model_file), + "--config", + tiny_config, + "--output", + str(output_filename), + str(mgf_small), + str(mzml_small), + "--evaluate", + ] + + result = run(eval_args) + assert result.exit_code == 0 + assert output_filename.is_file() + + mztab = pyteomics.mztab.MzTab(str(output_filename)) + # Verify that both input peak files are listed in the metadata. + for i, filename in enumerate(["small.mgf"], 1): + assert f"ms_run[{i}]-location" in mztab.metadata + assert mztab.metadata[f"ms_run[{i}]-location"].endswith(filename) + + # Verify that the spectrum predictions are correct + # and indexed according to the peak input file type. + psms = mztab.spectrum_match_table + assert psms.loc[1, "sequence"] == "LESLLEK" + assert psms.loc[1, "spectra_ref"] == "ms_run[1]:index=0" + assert psms.loc[2, "sequence"] == "PEPTLDEK" + assert psms.loc[2, "spectra_ref"] == "ms_run[1]:index=1" + # Validate mztab output validate_args = [ "java", diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index b39c3758..b64254bc 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -56,6 +56,7 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): config.max_epochs = 1 config.n_layers = 1 ckpt = tmp_path / "test.ckpt" + output_file = tmp_path / "out" with ModelRunner(config=config) as runner: runner.train([mgf_small], [mgf_small]) @@ -83,7 +84,7 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): with torch.device("meta"): with ModelRunner(other_config, model_filename=str(ckpt)) as runner: with pytest.raises(NotImplementedError) as err: - runner.evaluate([mgf_small]) + runner.predict([mgf_small], output_file, evaluate=True) assert "meta tensor; no data!" in str(err.value) @@ -95,11 +96,11 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): # Shouldn't work: with ModelRunner(other_config, model_filename=str(ckpt)) as runner: with pytest.raises(RuntimeError): - runner.evaluate([mgf_small]) + runner.predict([mgf_small], output_file, evaluate=True) # Should work: with ModelRunner(config=config, model_filename=str(ckpt)) as runner: - runner.evaluate([mgf_small]) + runner.predict([mgf_small], output_file, evaluate=True) def test_save_and_load_weights_deprecated(tmp_path, mgf_small, tiny_config): diff --git a/tests/unit_tests/test_unit.py b/tests/unit_tests/test_unit.py index 120e341a..b928ab4e 100644 --- a/tests/unit_tests/test_unit.py +++ b/tests/unit_tests/test_unit.py @@ -895,10 +895,11 @@ def test_train_val_step_functions(): spectra = torch.zeros(1, 5, 2) precursors = torch.tensor([[469.25364, 2.0, 235.63410]]) peptides = ["PEPK"] - batch = (spectra, precursors, peptides) + spectrum_id = "foobar" + batch = (spectra, precursors, spectrum_id, peptides) train_step_loss = model.training_step(batch) - val_step_loss = model.validation_step(batch) + val_step_loss, _ = model.validation_step(batch) # Check if valid loss value returned assert train_step_loss > 0 From d9b6f4877e742ec2249542e8f050a9e2552aade7 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Wed, 31 Jul 2024 11:07:47 -0700 Subject: [PATCH 25/36] updated documentation --- casanovo/data/datasets.py | 7 ++++++- casanovo/denovo/dataloaders.py | 12 ++++++++---- casanovo/denovo/model.py | 4 ++-- casanovo/denovo/model_runner.py | 6 +++++- 4 files changed, 21 insertions(+), 8 deletions(-) diff --git a/casanovo/data/datasets.py b/casanovo/data/datasets.py index f7b2fe7e..bd3d93af 100644 --- a/casanovo/data/datasets.py +++ b/casanovo/data/datasets.py @@ -235,7 +235,9 @@ def __init__( random_state=random_state, ) - def __getitem__(self, idx: int) -> Tuple[torch.Tensor, float, int, str]: + def __getitem__( + self, idx: int + ) -> Tuple[torch.Tensor, float, int, Tuple[str, str], str]: """ Return the annotated MS/MS spectrum with the given index. @@ -252,6 +254,9 @@ def __getitem__(self, idx: int) -> Tuple[torch.Tensor, float, int, str]: The precursor m/z. precursor_charge : int The precursor charge. + spectrum_id: Tuple[str, str] + The unique spectrum identifier, formed by its original peak file and + identifier (index or scan number) therein. annotation : str The peptide annotation of the spectrum. """ diff --git a/casanovo/denovo/dataloaders.py b/casanovo/denovo/dataloaders.py index ba58d83c..9a8b1e32 100644 --- a/casanovo/denovo/dataloaders.py +++ b/casanovo/denovo/dataloaders.py @@ -175,8 +175,8 @@ def predict_dataloader(self) -> torch.utils.data.DataLoader: def prepare_batch( - batch: List[Tuple[torch.Tensor, float, int, str]] -) -> Tuple[torch.Tensor, torch.Tensor, np.ndarray]: + batch: List[Tuple[torch.Tensor, float, int, str, Optional[str]]] +) -> Tuple[torch.Tensor, torch.Tensor, np.ndarray, np.ndarray | None]: """ Collate MS/MS spectra into a batch. @@ -185,10 +185,11 @@ def prepare_batch( Parameters ---------- - batch : List[Tuple[torch.Tensor, float, int, str]] + batch : List[Tuple[torch.Tensor, float, int, str, Optional[str]]] A batch of data from an AnnotatedSpectrumDataset, consisting of for each spectrum (i) a tensor with the m/z and intensity peak values, (ii), the - precursor m/z, (iii) the precursor charge, (iv) the spectrum identifier. + precursor m/z, (iii) the precursor charge, (iv) the spectrum identifier, + (v) optionally the peptide sequence annotation Returns ------- @@ -201,6 +202,9 @@ def prepare_batch( spectrum_ids : np.ndarray The spectrum identifiers (during de novo sequencing) or peptide sequences (during training). + annotations : np.ndarray | None + The peptide annotations of the spectra if provided by the dataset, + None otherwise """ batch_list = list(zip(*batch)) spectra, precursor_mzs, precursor_charges, spectrum_ids = batch_list[0:4] diff --git a/casanovo/denovo/model.py b/casanovo/denovo/model.py index 29acaf40..aae8d925 100644 --- a/casanovo/denovo/model.py +++ b/casanovo/denovo/model.py @@ -773,7 +773,7 @@ def validation_step( ---------- batch : Tuple[torch.Tensor, torch.Tensor, List[str]] A batch of (i) MS/MS spectra, (ii) precursor information, (iii) - peptide sequences. + spectrum identifiers, (iv) peptide sequence annotations Returns ------- @@ -788,7 +788,7 @@ def validation_step( # Calculate and log amino acid and peptide match evaluation metrics from # the predicted peptides. - peptides_pred, peptides_true = [], batch[2] + peptides_pred, peptides_true = [], batch[3] for spectrum_preds in forward_step: for _, _, pred in spectrum_preds: peptides_pred.append(pred) diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 083a0ace..523a4e60 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -123,6 +123,9 @@ def predict( ) -> None: """Predict peptide sequences with a trained Casanovo model. + Can also evaluate model during prediction if provided with annotated + peak files. + Parameters ---------- peak_path : iterable of str @@ -132,7 +135,8 @@ def predict( evaluate: str whether to run model evaluation in addition to inference Note: peak_path most point to annotated MS data files when - running model evaluation + running model evaluation. Files that are not an annotated + peak file format will be ignored if evaluate is set to true. Returns ------- From f441034d94e06c107a3c7d93dcb57842b87b9245 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Wed, 31 Jul 2024 11:20:53 -0700 Subject: [PATCH 26/36] removed log and result files --- bar.mztab | 189 ----------------------------------------------------- bar2.mztab | 189 ----------------------------------------------------- foo.mztab | 189 ----------------------------------------------------- foo2.mztab | 189 ----------------------------------------------------- 4 files changed, 756 deletions(-) delete mode 100644 bar.mztab delete mode 100644 bar2.mztab delete mode 100644 foo.mztab delete mode 100644 foo2.mztab diff --git a/bar.mztab b/bar.mztab deleted file mode 100644 index cbcd1bb5..00000000 --- a/bar.mztab +++ /dev/null @@ -1,189 +0,0 @@ -MTD mzTab-version 1.0.0 -MTD mzTab-mode Summary -MTD mzTab-type Identification -MTD description Casanovo identification file bar -MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] -MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] -MTD fixed_mod[1]-site C -MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[1]-site N -MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[2]-site Q -MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] -MTD variable_mod[3]-site M -MTD variable_mod[4] [UNIMOD, UNIMOD:5, Carbamyl, ] -MTD variable_mod[4]-site N-term -MTD variable_mod[5] [UNIMOD, UNIMOD:385, Ammonia-loss, ] -MTD variable_mod[5]-site N-term -MTD variable_mod[6] [UNIMOD, UNIMOD:1, Acetyl, ] -MTD variable_mod[6]-site N-term -MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt -MTD software[1]-setting[2] config_filename = default -MTD software[1]-setting[3] precursor_mass_tol = 50.0 -MTD software[1]-setting[4] isotope_error_range = (0, 1) -MTD software[1]-setting[5] min_peptide_len = 6 -MTD software[1]-setting[6] predict_batch_size = 1024 -MTD software[1]-setting[7] n_beams = 1 -MTD software[1]-setting[8] top_match = 1 -MTD software[1]-setting[9] accelerator = auto -MTD software[1]-setting[10] devices = None -MTD software[1]-setting[11] random_seed = 454 -MTD software[1]-setting[12] n_log = 1 -MTD software[1]-setting[13] tb_summarywriter = None -MTD software[1]-setting[14] save_top_k = 5 -MTD software[1]-setting[15] model_save_folder_path = -MTD software[1]-setting[16] val_check_interval = 50000 -MTD software[1]-setting[17] n_peaks = 150 -MTD software[1]-setting[18] min_mz = 50.0 -MTD software[1]-setting[19] max_mz = 2500.0 -MTD software[1]-setting[20] min_intensity = 0.01 -MTD software[1]-setting[21] remove_precursor_tol = 2.0 -MTD software[1]-setting[22] max_charge = 10 -MTD software[1]-setting[23] dim_model = 512 -MTD software[1]-setting[24] n_head = 8 -MTD software[1]-setting[25] dim_feedforward = 1024 -MTD software[1]-setting[26] n_layers = 9 -MTD software[1]-setting[27] dropout = 0.0 -MTD software[1]-setting[28] dim_intensity = None -MTD software[1]-setting[29] max_length = 100 -MTD software[1]-setting[30] warmup_iters = 100000 -MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 -MTD software[1]-setting[32] learning_rate = 0.0005 -MTD software[1]-setting[33] weight_decay = 1e-05 -MTD software[1]-setting[34] train_label_smoothing = 0.01 -MTD software[1]-setting[35] train_batch_size = 32 -MTD software[1]-setting[36] max_epochs = 30 -MTD software[1]-setting[37] num_sanity_val_steps = 0 -MTD software[1]-setting[38] calculate_precision = False -MTD software[1]-setting[40] n_workers = 0 -MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf -PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores -PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 -PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 -PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 -PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 -PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 -PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 -PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 -PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 -PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 -PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 -PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 -PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 -PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 -PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 -PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 -PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9672952890396118 null null 2 614.33795 614.33821831688 ms_run[1]:index=15 null null null null 0.97399,0.97959,0.97837,0.97845,0.96474,0.84979,0.97928,0.97613,0.97886,0.97760,0.97960,0.97994 -PSM LQEEERER 17 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.975036793284946 null null 2 544.77 544.77017681688 ms_run[1]:index=16 null null null null 0.91222,0.98079,0.98579,0.98252,0.98429,0.98225,0.98285,0.98220 -PSM TRGHESEMK 18 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1844959855079651 null null 2 539.25323 537.75346831688 ms_run[1]:index=17 null null null null 0.90297,0.90465,0.82135,0.90041,0.64139,0.62194,0.66087,0.89718,0.90124 -PSM +42.011KVEDPPRK 19 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.24581749439239498 null null 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0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 -PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 -PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 -PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 -PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 -PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 -PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 -PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 -PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 -PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 -PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 -PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 -PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 -PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 -PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 -PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 -PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 diff --git a/bar2.mztab b/bar2.mztab deleted file mode 100644 index 78f5939c..00000000 --- a/bar2.mztab +++ /dev/null @@ -1,189 +0,0 @@ -MTD mzTab-version 1.0.0 -MTD mzTab-mode Summary -MTD mzTab-type Identification -MTD description Casanovo identification file bar2 -MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] -MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] -MTD fixed_mod[1]-site C -MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[1]-site N -MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[2]-site Q -MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] -MTD variable_mod[3]-site M -MTD variable_mod[4] [UNIMOD, UNIMOD:385, Ammonia-loss, ] -MTD variable_mod[4]-site N-term -MTD variable_mod[5] [UNIMOD, UNIMOD:5, Carbamyl, ] -MTD variable_mod[5]-site N-term -MTD variable_mod[6] [UNIMOD, UNIMOD:1, Acetyl, ] -MTD variable_mod[6]-site N-term -MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt -MTD software[1]-setting[2] config_filename = default -MTD software[1]-setting[3] precursor_mass_tol = 50.0 -MTD software[1]-setting[4] isotope_error_range = (0, 1) -MTD software[1]-setting[5] min_peptide_len = 6 -MTD software[1]-setting[6] predict_batch_size = 1024 -MTD software[1]-setting[7] n_beams = 1 -MTD software[1]-setting[8] top_match = 1 -MTD software[1]-setting[9] accelerator = auto -MTD software[1]-setting[10] devices = None -MTD software[1]-setting[11] random_seed = 454 -MTD software[1]-setting[12] n_log = 1 -MTD software[1]-setting[13] tb_summarywriter = None -MTD software[1]-setting[14] save_top_k = 5 -MTD software[1]-setting[15] model_save_folder_path = -MTD software[1]-setting[16] val_check_interval = 50000 -MTD software[1]-setting[17] n_peaks = 150 -MTD software[1]-setting[18] min_mz = 50.0 -MTD software[1]-setting[19] max_mz = 2500.0 -MTD software[1]-setting[20] min_intensity = 0.01 -MTD software[1]-setting[21] remove_precursor_tol = 2.0 -MTD software[1]-setting[22] max_charge = 10 -MTD software[1]-setting[23] dim_model = 512 -MTD software[1]-setting[24] n_head = 8 -MTD software[1]-setting[25] dim_feedforward = 1024 -MTD software[1]-setting[26] n_layers = 9 -MTD software[1]-setting[27] dropout = 0.0 -MTD software[1]-setting[28] dim_intensity = None -MTD software[1]-setting[29] max_length = 100 -MTD software[1]-setting[30] warmup_iters = 100000 -MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 -MTD software[1]-setting[32] learning_rate = 0.0005 -MTD software[1]-setting[33] weight_decay = 1e-05 -MTD software[1]-setting[34] train_label_smoothing = 0.01 -MTD software[1]-setting[35] train_batch_size = 32 -MTD software[1]-setting[36] max_epochs = 30 -MTD software[1]-setting[37] num_sanity_val_steps = 0 -MTD software[1]-setting[38] calculate_precision = False -MTD software[1]-setting[40] n_workers = 0 -MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf -PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores -PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 -PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 -PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 -PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 -PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 -PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 -PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 -PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 -PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 -PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 -PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 -PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 -PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 -PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 -PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 -PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9672952890396118 null null 2 614.33795 614.33821831688 ms_run[1]:index=15 null null null null 0.97399,0.97959,0.97837,0.97845,0.96474,0.84979,0.97928,0.97613,0.97886,0.97760,0.97960,0.97994 -PSM LQEEERER 17 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.975036793284946 null null 2 544.77 544.77017681688 ms_run[1]:index=16 null null null null 0.91222,0.98079,0.98579,0.98252,0.98429,0.98225,0.98285,0.98220 -PSM TRGHESEMK 18 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1844959855079651 null null 2 539.25323 537.75346831688 ms_run[1]:index=17 null null null null 0.90297,0.90465,0.82135,0.90041,0.64139,0.62194,0.66087,0.89718,0.90124 -PSM +42.011KVEDPPRK 19 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.24581749439239498 null null 2 507.26154 505.78509881688007 ms_run[1]:index=18 null null null null 0.77158,0.66196,0.86775,0.87090,0.70578,0.61787,0.85217,0.69678,0.62489 -PSM TESPAEGKQEEEK 20 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.868788189121655 null null 2 731.3395 731.3388133168802 ms_run[1]:index=19 null null null null 0.92347,0.91621,0.74657,0.61987,0.87546,0.65200,0.92947,0.92629,0.93151,0.92995,0.92921,0.92534,0.92826 -PSM LVEEETKK 21 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879584113756815 null null 2 488.27112 488.27148531688005 ms_run[1]:index=20 null null null null 0.98623,0.98691,0.98852,0.98742,0.98734,0.98694,0.99077,0.98849 -PSM KAETLGEK 22 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9864536391364204 null null 2 438.24524 438.24527081688 ms_run[1]:index=21 null null null null 0.98740,0.98704,0.98770,0.98844,0.98931,0.98661,0.98774,0.97524 -PSM C+57.021LKPNETK 23 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9895809359020658 null null 2 495.25775 495.25785531688 ms_run[1]:index=22 null null null null 0.98927,0.98929,0.98595,0.99043,0.99001,0.99081,0.98784,0.99231 -PSM GHQALER 24 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9861482679843903 null null 2 405.71454 405.71447681688 ms_run[1]:index=23 null null null null 0.98369,0.97763,0.98807,0.98786,0.98838,0.98693,0.98818 -PSM TNNLRPK 25 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9859854802489281 null null 2 421.74548 421.74577181688005 ms_run[1]:index=24 null null null null 0.98893,0.99008,0.98974,0.98259,0.98795,0.97375,0.98633 -PSM +43.006DTPGHATPGHGAGTQER 26 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.22608531070382976 null null 2 867.40045 866.39330131688 ms_run[1]:index=25 null null null null 0.85561,0.57927,0.49126,0.50495,0.70489,0.76038,0.75372,0.53050,0.87917,0.87740,0.88139,0.87799,0.88406,0.88016,0.88217,0.87672,0.82864,0.77355 -PSM KSYTTPK 27 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8933427818119526 null null 2 412.72778 412.72925231688004 ms_run[1]:index=26 null null null null 0.93932,0.94376,0.93479,0.61684,0.94099,0.93574,0.89386 -PSM VLEGHAEK 28 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879539277818468 null null 2 441.73788 441.73761731688 ms_run[1]:index=27 null null null null 0.98716,0.98573,0.98970,0.98983,0.98921,0.98323,0.98926,0.98847 -PSM LQHEATAATQK 29 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9673882275819778 null null 2 599.3142 599.31474381688 ms_run[1]:index=28 null null null null 0.97810,0.97690,0.97761,0.96875,0.88905,0.98107,0.97901,0.94171,0.98001,0.97853,0.97914 -PSM KEAPAPPK 30 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.99110433128145 null null 2 419.24496 419.24507831688004 ms_run[1]:index=29 null null null null 0.98966,0.99341,0.99059,0.99097,0.99120,0.99191,0.99078,0.99143 -PSM ERDELR 31 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9874146069799151 null null 2 409.2106 409.2117663168801 ms_run[1]:index=30 null null null null 0.98921,0.98706,0.98802,0.98241,0.98891,0.98739 -PSM EVLHANNR 32 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8818797965844473 null null 2 476.75156 476.75158981687997 ms_run[1]:index=31 null null null null 0.93772,0.73514,0.67541,0.93265,0.93705,0.93603,0.93502,0.91176 -PSM NNTLTPNKPNK 33 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1514618446429571 null null 2 613.8276 620.83584181688 ms_run[1]:index=32 null null null null 0.90068,0.80453,0.91917,0.67357,0.80102,0.91849,0.91801,0.71365,0.91622,0.90961,0.78907 -PSM MQEHMR 34 null null 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LYPGHGR 84 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9855495616793633 null null 2 400.2142 400.21411281688 ms_run[1]:index=83 null null null null 0.98857,0.97604,0.99047,0.98599,0.98512,0.98456,0.98545 -PSM LANREDEYKK 85 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7523967054757205 null null 2 633.81976 633.3278588168799 ms_run[1]:index=84 null null null null 0.87074,0.87165,0.87060,0.87076,0.83804,0.59388,0.46819,0.54366,0.60789,0.86938 -PSM QHTEQEASGYR 86 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9599030663569769 null null 2 653.29474 653.2945438168799 ms_run[1]:index=85 null null null null 0.96870,0.83809,0.97494,0.97507,0.97362,0.96334,0.97149,0.96726,0.97383,0.97369,0.96378 -PSM RGFYNGTK 87 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1575217843055725 null null 2 479.74063 471.74322981688005 ms_run[1]:index=86 null null null null 0.91292,0.91689,0.91616,0.91850,0.91859,0.62517,0.58075,0.87869 -PSM ATKPLENELSRK 88 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7837637743124595 null null 2 693.391 693.39098581688 ms_run[1]:index=87 null null null null 0.88423,0.56842,0.49764,0.48800,0.69792,0.86291,0.88665,0.88700,0.88647,0.87839,0.87596,0.88848 -PSM VTLTNHK 89 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9906119257211685 null null 2 406.73508 406.73486881688 ms_run[1]:index=88 null null null null 0.99117,0.99167,0.99138,0.98946,0.99058,0.99082,0.98972 -PSM KQVHPDTGLSSK 90 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.784689323260234 null null 2 648.8487 648.84895431688 ms_run[1]:index=89 null null null null 0.88510,0.86906,0.88436,0.60227,0.56352,0.73759,0.86867,0.88519,0.88925,0.58474,0.65597,0.88862 -PSM ALHVNNDR 91 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9739643534024557 null null 2 469.74402 469.74376481687995 ms_run[1]:index=90 null null null null 0.98300,0.94303,0.94576,0.98170,0.98200,0.98309,0.98087,0.98429 -PSM HQGVDVSQGQK 92 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.2755244250098864 null null 2 602.2881 591.7967268168799 ms_run[1]:index=91 null null null null 0.81014,0.61340,0.85479,0.55058,0.51206,0.80981,0.52666,0.74098,0.72937,0.84537,0.84671 -PSM KDQLADAR 93 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9833353890313042 null null 2 458.74606 458.74597381688005 ms_run[1]:index=92 null null null null 0.98578,0.98789,0.96864,0.98753,0.98707,0.98619,0.97211,0.98784 -PSM AGM+15.995THLVR 94 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9909310738245646 null null 2 450.73972 450.73963331688 ms_run[1]:index=93 null null null null 0.98624,0.99125,0.99075,0.99034,0.99038,0.99374,0.99342,0.99157 -PSM VC+57.021ETDTEC+57.021EAK 95 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8007588014006615 null null 2 671.7649 671.26848431688 ms_run[1]:index=94 null null null null 0.85310,0.86264,0.63520,0.51281,0.54561,0.89137,0.87732,0.89623,0.89416,0.85729,0.88848 -PSM DNEEETTDDPRK 96 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9748788430140569 null null 2 724.8101 724.81041531688 ms_run[1]:index=95 null null null null 0.97278,0.97866,0.98283,0.94063,0.97179,0.98396,0.98175,0.97949,0.97996,0.98068,0.96405,0.97450 -PSM LATENSTQAQSK 97 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8541486240350283 null null 2 639.3202 639.32022231688 ms_run[1]:index=96 null null null null 0.91946,0.88310,0.64405,0.91759,0.61508,0.70209,0.92141,0.92149,0.91321,0.92107,0.90086,0.92215 -PSM SVHELEK 98 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9886416047811508 null null 2 421.2242 421.22434231688004 ms_run[1]:index=97 null null null null 0.98951,0.98664,0.98892,0.98538,0.98991,0.98926,0.99082 -PSM SGTATAANPAEM+15.995YK 99 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6758072773615519 null null 2 714.3115 714.32719081688 ms_run[1]:index=98 null null null null 0.49935,0.43461,0.57078,0.53960,0.56327,0.81141,0.63182,0.67101,0.83289,0.79074,0.74597,0.62813,0.74957,0.83457 -PSM +42.011SGEELRK 100 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.15170641077889335 null null 2 437.25616 430.7272493168801 ms_run[1]:index=99 null null null null 0.85811,0.91444,0.88994,0.69713,0.91029,0.88104,0.68493,0.87894 -PSM TSYAQHQQVR 101 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.989588509906422 null null 2 609.3046 609.3047148168799 ms_run[1]:index=100 null null null null 0.99056,0.99011,0.98729,0.98997,0.99053,0.98848,0.98996,0.98965,0.99105,0.98859 -PSM NDEELNK 102 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9784338027238846 null null 2 431.2012 431.20106381688004 ms_run[1]:index=101 null null null null 0.98508,0.98284,0.98438,0.97530,0.97293,0.96303,0.97950 -PSM GGSLPQNHLHGH 103 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7780202948130094 null null 2 627.3102 627.3103353168799 ms_run[1]:index=102 null null null null 0.88073,0.88552,0.88639,0.53989,0.48982,0.59155,0.75677,0.88470,0.79813,0.81800,0.81249,0.88578 -PSM EESGKPQHVTVK 104 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9577845564255347 null null 2 669.8538 669.85423681688 ms_run[1]:index=103 null null null null 0.97224,0.97328,0.97316,0.97085,0.97283,0.78519,0.97378,0.96353,0.97323,0.97306,0.97223,0.97381 -PSM NSYTN+0.984GHSSDK 105 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6759249443809191 null null 2 605.7616 605.75217631688 ms_run[1]:index=104 null null null null 0.80744,0.47209,0.48691,0.43885,0.55379,0.57064,0.61858,0.83322,0.82685,0.83470,0.83499 -PSM APTQGEC+57.021HC+57.021DQTF 106 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6652015820145607 null null 2 775.8415 775.8035578168799 ms_run[1]:index=105 null null null null 0.42189,0.79374,0.76732,0.44555,0.50619,0.52009,0.46332,0.59417,0.82448,0.66210,0.82893,0.82902,0.82790 -PSM NVHELEK 107 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9881609752774239 null null 2 434.7295 434.72979181688004 ms_run[1]:index=106 null null null null 0.98844,0.98742,0.98892,0.98666,0.98955,0.98984,0.98553 -PSM YPNHSVDR 108 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9701713191138374 null null 2 494.2362 494.23577281688 ms_run[1]:index=107 null null null null 0.98136,0.88748,0.97896,0.98037,0.98181,0.97936,0.98056,0.98167 -PSM NKEGEVDYAK 109 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8123747543855147 null null 2 576.78033 576.7802103168799 ms_run[1]:index=108 null null null null 0.90083,0.90001,0.89895,0.59818,0.57671,0.56759,0.90301,0.89488,0.90020,0.89448 -PSM LRPEPNTGK 110 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.052142149209976174 null null 2 499.27567 506.28271881688005 ms_run[1]:index=109 null null null null 0.96482,0.96376,0.96742,0.96250,0.96909,0.84115,0.96040,0.94795,0.93244 -PSM NN+0.984EELNK 111 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20876559987664223 null null 2 421.71188 431.20106381688004 ms_run[1]:index=110 null null null null 0.89154,0.89164,0.89013,0.88795,0.88142,0.61297,0.87860 -PSM PHESNYEEDGK 112 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3362173897524675 null null 2 646.7648 652.77311331688 ms_run[1]:index=111 null null null null 0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 -PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 -PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 -PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 -PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 -PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 -PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 -PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 -PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 -PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 -PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 -PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 -PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 -PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 -PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 -PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 -PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 diff --git a/foo.mztab b/foo.mztab deleted file mode 100644 index aa8a6922..00000000 --- a/foo.mztab +++ /dev/null @@ -1,189 +0,0 @@ -MTD mzTab-version 1.0.0 -MTD mzTab-mode Summary -MTD mzTab-type Identification -MTD description Casanovo identification file foo -MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] -MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] -MTD fixed_mod[1]-site C -MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[1]-site N -MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[2]-site Q -MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] -MTD variable_mod[3]-site M -MTD variable_mod[4] [UNIMOD, UNIMOD:5, Carbamyl, ] -MTD variable_mod[4]-site N-term -MTD variable_mod[5] [UNIMOD, UNIMOD:1, Acetyl, ] -MTD variable_mod[5]-site N-term -MTD variable_mod[6] [UNIMOD, UNIMOD:385, Ammonia-loss, ] -MTD variable_mod[6]-site N-term -MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt -MTD software[1]-setting[2] config_filename = default -MTD software[1]-setting[3] precursor_mass_tol = 50.0 -MTD software[1]-setting[4] isotope_error_range = (0, 1) -MTD software[1]-setting[5] min_peptide_len = 6 -MTD software[1]-setting[6] predict_batch_size = 1024 -MTD software[1]-setting[7] n_beams = 1 -MTD software[1]-setting[8] top_match = 1 -MTD software[1]-setting[9] accelerator = auto -MTD software[1]-setting[10] devices = None -MTD software[1]-setting[11] random_seed = 454 -MTD software[1]-setting[12] n_log = 1 -MTD software[1]-setting[13] tb_summarywriter = None -MTD software[1]-setting[14] save_top_k = 5 -MTD software[1]-setting[15] model_save_folder_path = -MTD software[1]-setting[16] val_check_interval = 50000 -MTD software[1]-setting[17] n_peaks = 150 -MTD software[1]-setting[18] min_mz = 50.0 -MTD software[1]-setting[19] max_mz = 2500.0 -MTD software[1]-setting[20] min_intensity = 0.01 -MTD software[1]-setting[21] remove_precursor_tol = 2.0 -MTD software[1]-setting[22] max_charge = 10 -MTD software[1]-setting[23] dim_model = 512 -MTD software[1]-setting[24] n_head = 8 -MTD software[1]-setting[25] dim_feedforward = 1024 -MTD software[1]-setting[26] n_layers = 9 -MTD software[1]-setting[27] dropout = 0.0 -MTD software[1]-setting[28] dim_intensity = None -MTD software[1]-setting[29] max_length = 100 -MTD software[1]-setting[30] warmup_iters = 100000 -MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 -MTD software[1]-setting[32] learning_rate = 0.0005 -MTD software[1]-setting[33] weight_decay = 1e-05 -MTD software[1]-setting[34] train_label_smoothing = 0.01 -MTD software[1]-setting[35] train_batch_size = 32 -MTD software[1]-setting[36] max_epochs = 30 -MTD software[1]-setting[37] num_sanity_val_steps = 0 -MTD software[1]-setting[38] calculate_precision = False -MTD software[1]-setting[40] n_workers = 0 -MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf -PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores -PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 -PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 -PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 -PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 -PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 -PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 -PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 -PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 -PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 -PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 -PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 -PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 -PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 -PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 -PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 -PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9672952890396118 null null 2 614.33795 614.33821831688 ms_run[1]:index=15 null null null null 0.97399,0.97959,0.97837,0.97845,0.96474,0.84979,0.97928,0.97613,0.97886,0.97760,0.97960,0.97994 -PSM LQEEERER 17 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.975036793284946 null null 2 544.77 544.77017681688 ms_run[1]:index=16 null null null null 0.91222,0.98079,0.98579,0.98252,0.98429,0.98225,0.98285,0.98220 -PSM TRGHESEMK 18 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1844959855079651 null null 2 539.25323 537.75346831688 ms_run[1]:index=17 null null null null 0.90297,0.90465,0.82135,0.90041,0.64139,0.62194,0.66087,0.89718,0.90124 -PSM +42.011KVEDPPRK 19 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.24581749439239498 null null 2 507.26154 505.78509881688007 ms_run[1]:index=18 null null null null 0.77158,0.66196,0.86775,0.87090,0.70578,0.61787,0.85217,0.69678,0.62489 -PSM TESPAEGKQEEEK 20 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.868788189121655 null null 2 731.3395 731.3388133168802 ms_run[1]:index=19 null null null null 0.92347,0.91621,0.74657,0.61987,0.87546,0.65200,0.92947,0.92629,0.93151,0.92995,0.92921,0.92534,0.92826 -PSM LVEEETKK 21 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879584113756815 null null 2 488.27112 488.27148531688005 ms_run[1]:index=20 null null null null 0.98623,0.98691,0.98852,0.98742,0.98734,0.98694,0.99077,0.98849 -PSM KAETLGEK 22 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9864536391364204 null null 2 438.24524 438.24527081688 ms_run[1]:index=21 null null null null 0.98740,0.98704,0.98770,0.98844,0.98931,0.98661,0.98774,0.97524 -PSM C+57.021LKPNETK 23 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9895809359020658 null null 2 495.25775 495.25785531688 ms_run[1]:index=22 null null null null 0.98927,0.98929,0.98595,0.99043,0.99001,0.99081,0.98784,0.99231 -PSM GHQALER 24 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9861482679843903 null null 2 405.71454 405.71447681688 ms_run[1]:index=23 null null null null 0.98369,0.97763,0.98807,0.98786,0.98838,0.98693,0.98818 -PSM TNNLRPK 25 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9859854802489281 null null 2 421.74548 421.74577181688005 ms_run[1]:index=24 null null null null 0.98893,0.99008,0.98974,0.98259,0.98795,0.97375,0.98633 -PSM +43.006DTPGHATPGHGAGTQER 26 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.22608531070382976 null null 2 867.40045 866.39330131688 ms_run[1]:index=25 null null null null 0.85561,0.57927,0.49126,0.50495,0.70489,0.76038,0.75372,0.53050,0.87917,0.87740,0.88139,0.87799,0.88406,0.88016,0.88217,0.87672,0.82864,0.77355 -PSM KSYTTPK 27 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8933427818119526 null null 2 412.72778 412.72925231688004 ms_run[1]:index=26 null null null null 0.93932,0.94376,0.93479,0.61684,0.94099,0.93574,0.89386 -PSM VLEGHAEK 28 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9879539277818468 null null 2 441.73788 441.73761731688 ms_run[1]:index=27 null null null null 0.98716,0.98573,0.98970,0.98983,0.98921,0.98323,0.98926,0.98847 -PSM LQHEATAATQK 29 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9673882275819778 null null 2 599.3142 599.31474381688 ms_run[1]:index=28 null null null null 0.97810,0.97690,0.97761,0.96875,0.88905,0.98107,0.97901,0.94171,0.98001,0.97853,0.97914 -PSM KEAPAPPK 30 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.99110433128145 null null 2 419.24496 419.24507831688004 ms_run[1]:index=29 null null null null 0.98966,0.99341,0.99059,0.99097,0.99120,0.99191,0.99078,0.99143 -PSM ERDELR 31 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9874146069799151 null null 2 409.2106 409.2117663168801 ms_run[1]:index=30 null null null null 0.98921,0.98706,0.98802,0.98241,0.98891,0.98739 -PSM EVLHANNR 32 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8818797965844473 null null 2 476.75156 476.75158981687997 ms_run[1]:index=31 null null null null 0.93772,0.73514,0.67541,0.93265,0.93705,0.93603,0.93502,0.91176 -PSM NNTLTPNKPNK 33 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.1514618446429571 null null 2 613.8276 620.83584181688 ms_run[1]:index=32 null null null null 0.90068,0.80453,0.91917,0.67357,0.80102,0.91849,0.91801,0.71365,0.91622,0.90961,0.78907 -PSM MQEHMR 34 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894828966685704 null null 2 416.18372 416.18364081688 ms_run[1]:index=33 null null null null 0.98712,0.98906,0.99189,0.98772,0.99073,0.98986 -PSM HNSYTAC+57.021ETHK 35 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8552879715959231 null null 2 674.29083 674.29094231688 ms_run[1]:index=34 null null null null 0.91161,0.92276,0.92215,0.75983,0.57698,0.64840,0.90726,0.92049,0.92356,0.92284,0.92449 -PSM WAPGHATPFSDESSSR 36 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43844590730526867 null null 2 867.4 866.3897028168802 ms_run[1]:index=35 null null null null 0.62368,0.35030,0.34498,0.43399,0.63293,0.39463,0.54277,0.45963,0.77829,0.76285,0.61244,0.56565,0.66891,0.77050,0.38220,0.45175 -PSM GDDETLHK 37 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9814771148893568 null null 2 457.71384 457.71433481688 ms_run[1]:index=36 null null null null 0.98366,0.98677,0.98606,0.98567,0.97685,0.97706,0.96534,0.98540 -PSM NEKSEEEQSSASVK 38 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9875149647394816 null null 2 776.35913 776.3602803168801 ms_run[1]:index=37 null null null null 0.98915,0.98944,0.98834,0.98835,0.98850,0.98888,0.97847,0.98778,0.98852,0.98666,0.98830,0.98710,0.98650,0.98822 -PSM NNTVTPGGKPGGK 39 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.946726496730532 null null 2 613.82745 613.8280178168801 ms_run[1]:index=38 null null null null 0.93242,0.80678,0.95406,0.96786,0.88768,0.96598,0.96954,0.96820,0.96772,0.96757,0.96759,0.96293,0.96766 -PSM HNGEEEEETHK 40 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.4023066883285841 null null 2 674.2913 669.7814653168799 ms_run[1]:index=39 null null null null 0.79198,0.79514,0.76636,0.39427,0.42610,0.40046,0.40083,0.39425,0.44152,0.77926,0.78835 -PSM HDSVEER 41 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9554774761199951 null null 2 436.19864 436.1988558168801 ms_run[1]:index=40 null null null null 0.94772,0.95530,0.92708,0.94280,0.96933,0.95420,0.97425 -PSM EGGQVASMEEEK 42 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.48210483216322386 null null 2 648.29266 647.28499981688 ms_run[1]:index=41 null null null null 0.39005,0.43086,0.42453,0.34300,0.64313,0.48547,0.75237,0.73883,0.36843,0.39590,0.47632,0.52967 -PSM AVTKYTSSK 43 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865922451019287 null null 2 492.77188 492.77164831688003 ms_run[1]:index=42 null null null null 0.98637,0.98900,0.98957,0.98818,0.98921,0.98818,0.98726,0.97004,0.98958 -PSM TKYTSSK 44 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.977924220263958 null null 2 407.71896 407.71888431688 ms_run[1]:index=43 null null null null 0.98495,0.98298,0.98361,0.98325,0.98555,0.93525,0.98402 -PSM SSFSQHAR 45 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 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0.98951,0.98664,0.98892,0.98538,0.98991,0.98926,0.99082 -PSM SGTATAANPAEM+15.995YK 99 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6758072773615519 null null 2 714.3115 714.32719081688 ms_run[1]:index=98 null null null null 0.49935,0.43461,0.57078,0.53960,0.56327,0.81141,0.63182,0.67101,0.83289,0.79074,0.74597,0.62813,0.74957,0.83457 -PSM +42.011SGEELRK 100 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.15170641077889335 null null 2 437.25616 430.7272493168801 ms_run[1]:index=99 null null null null 0.85811,0.91444,0.88994,0.69713,0.91029,0.88104,0.68493,0.87894 -PSM TSYAQHQQVR 101 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.989588509906422 null null 2 609.3046 609.3047148168799 ms_run[1]:index=100 null null null null 0.99056,0.99011,0.98729,0.98997,0.99053,0.98848,0.98996,0.98965,0.99105,0.98859 -PSM NDEELNK 102 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9784338027238846 null null 2 431.2012 431.20106381688004 ms_run[1]:index=101 null null null null 0.98508,0.98284,0.98438,0.97530,0.97293,0.96303,0.97950 -PSM GGSLPQNHLHGH 103 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.7780202948130094 null null 2 627.3102 627.3103353168799 ms_run[1]:index=102 null null null null 0.88073,0.88552,0.88639,0.53989,0.48982,0.59155,0.75677,0.88470,0.79813,0.81800,0.81249,0.88578 -PSM EESGKPQHVTVK 104 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9577845564255347 null null 2 669.8538 669.85423681688 ms_run[1]:index=103 null null null null 0.97224,0.97328,0.97316,0.97085,0.97283,0.78519,0.97378,0.96353,0.97323,0.97306,0.97223,0.97381 -PSM NSYTN+0.984GHSSDK 105 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6759249443809191 null null 2 605.7616 605.75217631688 ms_run[1]:index=104 null null null null 0.80744,0.47209,0.48691,0.43885,0.55379,0.57064,0.61858,0.83322,0.82685,0.83470,0.83499 -PSM APTQGEC+57.021HC+57.021DQTF 106 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6652015820145607 null null 2 775.8415 775.8035578168799 ms_run[1]:index=105 null null null null 0.42189,0.79374,0.76732,0.44555,0.50619,0.52009,0.46332,0.59417,0.82448,0.66210,0.82893,0.82902,0.82790 -PSM NVHELEK 107 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9881609752774239 null null 2 434.7295 434.72979181688004 ms_run[1]:index=106 null null null null 0.98844,0.98742,0.98892,0.98666,0.98955,0.98984,0.98553 -PSM YPNHSVDR 108 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9701713191138374 null null 2 494.2362 494.23577281688 ms_run[1]:index=107 null null null null 0.98136,0.88748,0.97896,0.98037,0.98181,0.97936,0.98056,0.98167 -PSM NKEGEVDYAK 109 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8123747543855147 null null 2 576.78033 576.7802103168799 ms_run[1]:index=108 null null null null 0.90083,0.90001,0.89895,0.59818,0.57671,0.56759,0.90301,0.89488,0.90020,0.89448 -PSM LRPEPNTGK 110 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.052142149209976174 null null 2 499.27567 506.28271881688005 ms_run[1]:index=109 null null null null 0.96482,0.96376,0.96742,0.96250,0.96909,0.84115,0.96040,0.94795,0.93244 -PSM NN+0.984EELNK 111 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20876559987664223 null null 2 421.71188 431.20106381688004 ms_run[1]:index=110 null null null null 0.89154,0.89164,0.89013,0.88795,0.88142,0.61297,0.87860 -PSM PHESNYEEDGK 112 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3362173897524675 null null 2 646.7648 652.77311331688 ms_run[1]:index=111 null null null null 0.77834,0.82270,0.64850,0.56150,0.42750,0.44410,0.51128,0.48163,0.81500,0.82286,0.82509 -PSM NEEC+57.021C+57.021EM+15.995DTAAQK 113 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.43397948678050724 null null 2 804.3514 801.29745181688 ms_run[1]:index=112 null null null null 0.76930,0.50069,0.77490,0.45056,0.77527,0.41984,0.39032,0.43908,0.37063,0.73276,0.39633,0.38620,0.74059 -PSM GHVQPLR 114 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9894894734025002 null null 2 403.73557 403.73521231688 ms_run[1]:index=113 null null null null 0.99079,0.98984,0.98967,0.98817,0.98909,0.98910,0.98940 -PSM SQKPVVVK 115 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9902426600456238 null null 2 442.78156 442.78182781687997 ms_run[1]:index=114 null null null null 0.99036,0.99096,0.98909,0.99096,0.98947,0.99225,0.98915,0.98947 -PSM NPTYRPR 116 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9865992292761803 null null 2 452.2438 452.24339681687997 ms_run[1]:index=115 null null null null 0.97301,0.98921,0.99280,0.98770,0.98652,0.98867,0.98784 -PSM KYEEVAR 117 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9781770259141922 null null 2 447.7375 447.73761731688006 ms_run[1]:index=116 null null null null 0.98487,0.98515,0.98309,0.98251,0.97983,0.98598,0.93925 -PSM LGHDAYR 118 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9852376729249954 null null 2 416.20963 416.20902731688005 ms_run[1]:index=117 null null null null 0.98284,0.97732,0.98686,0.98449,0.98828,0.98749,0.98658 -PSM C+57.021FNKPEDK 119 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9868554075558981 null null 2 519.2398 519.23966681688 ms_run[1]:index=118 null null null null 0.98799,0.97772,0.98833,0.98948,0.98876,0.98795,0.98278,0.99025 -PSM AQHEDQVEQYKK 120 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 -PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 -PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 -PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 -PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 -PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 -PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 -PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 -PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 diff --git a/foo2.mztab b/foo2.mztab deleted file mode 100644 index c95f7791..00000000 --- a/foo2.mztab +++ /dev/null @@ -1,189 +0,0 @@ -MTD mzTab-version 1.0.0 -MTD mzTab-mode Summary -MTD mzTab-type Identification -MTD description Casanovo identification file foo2 -MTD software[1] [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -MTD psm_search_engine_score[1] [MS, MS:1001143, search engine specific score for PSMs, ] -MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ] -MTD fixed_mod[1]-site C -MTD variable_mod[1] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[1]-site N -MTD variable_mod[2] [UNIMOD, UNIMOD:7, Deamidated, ] -MTD variable_mod[2]-site Q -MTD variable_mod[3] [UNIMOD, UNIMOD:35, Oxidation, ] -MTD variable_mod[3]-site M -MTD variable_mod[4] [UNIMOD, UNIMOD:385, Ammonia-loss, ] -MTD variable_mod[4]-site N-term -MTD variable_mod[5] [UNIMOD, UNIMOD:1, Acetyl, ] -MTD variable_mod[5]-site N-term -MTD variable_mod[6] [UNIMOD, UNIMOD:5, Carbamyl, ] -MTD variable_mod[6]-site N-term -MTD software[1]-setting[1] model = C:\Users\gavin\AppData\Local\casanovo\casanovo_v420_v4_2_0.ckpt -MTD software[1]-setting[2] config_filename = default -MTD software[1]-setting[3] precursor_mass_tol = 50.0 -MTD software[1]-setting[4] isotope_error_range = (0, 1) -MTD software[1]-setting[5] min_peptide_len = 6 -MTD software[1]-setting[6] predict_batch_size = 1024 -MTD software[1]-setting[7] n_beams = 1 -MTD software[1]-setting[8] top_match = 1 -MTD software[1]-setting[9] accelerator = auto -MTD software[1]-setting[10] devices = None -MTD software[1]-setting[11] random_seed = 454 -MTD software[1]-setting[12] n_log = 1 -MTD software[1]-setting[13] tb_summarywriter = None -MTD software[1]-setting[14] save_top_k = 5 -MTD software[1]-setting[15] model_save_folder_path = -MTD software[1]-setting[16] val_check_interval = 50000 -MTD software[1]-setting[17] n_peaks = 150 -MTD software[1]-setting[18] min_mz = 50.0 -MTD software[1]-setting[19] max_mz = 2500.0 -MTD software[1]-setting[20] min_intensity = 0.01 -MTD software[1]-setting[21] remove_precursor_tol = 2.0 -MTD software[1]-setting[22] max_charge = 10 -MTD software[1]-setting[23] dim_model = 512 -MTD software[1]-setting[24] n_head = 8 -MTD software[1]-setting[25] dim_feedforward = 1024 -MTD software[1]-setting[26] n_layers = 9 -MTD software[1]-setting[27] dropout = 0.0 -MTD software[1]-setting[28] dim_intensity = None -MTD software[1]-setting[29] max_length = 100 -MTD software[1]-setting[30] warmup_iters = 100000 -MTD software[1]-setting[31] cosine_schedule_period_iters = 600000 -MTD software[1]-setting[32] learning_rate = 0.0005 -MTD software[1]-setting[33] weight_decay = 1e-05 -MTD software[1]-setting[34] train_label_smoothing = 0.01 -MTD software[1]-setting[35] train_batch_size = 32 -MTD software[1]-setting[36] max_epochs = 30 -MTD software[1]-setting[37] num_sanity_val_steps = 0 -MTD software[1]-setting[38] calculate_precision = False -MTD software[1]-setting[40] n_workers = 0 -MTD ms_run[1]-location file:///C:/Users/gavin/OneDrive/Documents/casanovo/sample_data/sample_preprocessed_spectra.mgf -PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications retention_time charge exp_mass_to_charge calc_mass_to_charge spectra_ref pre post start end opt_ms_run[1]_aa_scores -PSM LAHYNKR 1 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9853372052311897 null null 2 451.25348 451.25376881688004 ms_run[1]:index=0 null null null null 0.98607,0.97971,0.97939,0.98738,0.98816,0.98699,0.98691 -PSM VKEDPDGEAHR 2 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.926614465812842 null null 2 626.79913 626.79946581688 ms_run[1]:index=1 null null null null 0.94723,0.70290,0.95174,0.92511,0.95889,0.88985,0.95799,0.95736,0.95729,0.95428,0.95846 -PSM C+57.021GHTNNLRPK 3 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9823594472625039 null null 2 598.80054 598.80128431688 ms_run[1]:index=2 null null null null 0.98705,0.98812,0.98848,0.98474,0.98451,0.98257,0.98377,0.98392,0.95174,0.98776 -PSM VVQEQGTHPK 4 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.983969970182939 null null 2 561.7985 561.79873381688 ms_run[1]:index=3 null null null null 0.98777,0.98899,0.98769,0.95718,0.98781,0.98609,0.98126,0.98761,0.98634,0.98607 -PSM KGKPELR 5 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9804770648479462 null null 2 414.25836 414.2585198168801 ms_run[1]:index=4 null null null null 0.97140,0.98258,0.98577,0.98493,0.98646,0.96095,0.98719 -PSM SLSHSPGK 6 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9354224304358164 null null 2 406.71677 406.71668431688 ms_run[1]:index=5 null null null null 0.96445,0.96163,0.96387,0.96421,0.96337,0.96321,0.71570,0.95941 -PSM HNSYTC+57.021EATHK 7 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9893702119588852 null null 2 674.29034 674.29094231688 ms_run[1]:index=6 null null null null 0.98902,0.99101,0.98925,0.98902,0.98774,0.99066,0.99102,0.99000,0.99018,0.98493,0.98976 -PSM HNTEEC+57.021LTAHK 8 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3386161054174105 null null 3 449.86273 447.20682036688004 ms_run[1]:index=7 null null null null 0.82412,0.82579,0.66107,0.82137,0.44290,0.47984,0.40612,0.44921,0.65647,0.72212,0.82221 -PSM RPN+0.984SDAAATHK 9 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8276803915699323 null null 2 585.28577 584.7888968168799 ms_run[1]:index=8 null null null null 0.86920,0.90928,0.89751,0.87443,0.55649,0.86867,0.74169,0.71788,0.76890,0.90922,0.91056 -PSM KPANVVTK 10 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9407420423295763 null null 2 428.76614 428.76617331688004 ms_run[1]:index=9 null null null null 0.96079,0.96577,0.86124,0.87460,0.93816,0.96595,0.96657,0.96776 -PSM EKEELEK 11 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9468273594975471 null null 2 452.7346 452.73473981688005 ms_run[1]:index=10 null null null null 0.96895,0.96406,0.96898,0.96751,0.96714,0.91923,0.84989 -PSM FAEEDKK 12 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9831042215228081 null null 2 433.71643 433.71635031688004 ms_run[1]:index=11 null null null null 0.98641,0.98477,0.96714,0.98472,0.98062,0.98744,0.98673 -PSM TAVHTSTR 13 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8143551978800032 null null 2 436.73282 436.73285331688004 ms_run[1]:index=12 null null null null 0.90321,0.67999,0.90315,0.90186,0.90437,0.67515,0.65618,0.80327 -PSM AHGNM+15.995NVR 14 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.20804159508811104 null null 2 464.72443 457.71669331688 ms_run[1]:index=13 null null null null 0.88382,0.80939,0.65324,0.63238,0.71456,0.79177,0.87114,0.88125 -PSM KSPEPVR 15 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9892207086086273 null null 2 406.73514 406.73487731688004 ms_run[1]:index=14 null null null null 0.99070,0.98201,0.98937,0.99048,0.98930,0.98946,0.99215 -PSM HAVSEGTKAVTK 16 null null null null [MS, MS:1003281, Casanovo, 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MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.985522577395806 null null 2 751.86487 751.86533781688 ms_run[1]:index=119 null null null null 0.98871,0.98899,0.98811,0.98113,0.98533,0.98580,0.98276,0.98214,0.98626,0.98835,0.97737,0.98934 -PSM LSRPGDSDDSR 121 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8713361918926239 null null 2 602.7813 602.7812723168798 ms_run[1]:index=120 null null null null 0.75597,0.93132,0.90826,0.92920,0.92528,0.92121,0.71465,0.93131,0.87603,0.70035,0.93175 -PSM VPSPGFVGR 122 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.870770537853241 null null 2 458.25607 458.25597731688 ms_run[1]:index=121 null null null null 0.68682,0.82868,0.77559,0.83503,0.92990,0.92966,0.93123,0.93107,0.92943 -PSM +42.011VNVHQTELELDKR 123 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.6853616863489151 null null 2 812.4254 811.92846431688 ms_run[1]:index=122 null null null null 0.83714,0.80660,0.81681,0.44424,0.46244,0.46635,0.55756,0.83669,0.82390,0.81668,0.66397,0.61746,0.62706,0.66628 -PSM QGVLTHGR 124 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9900487661361694 null null 2 434.24365 434.24339731688 ms_run[1]:index=123 null null null null 0.99084,0.98976,0.99153,0.98966,0.99008,0.99051,0.98982,0.98833 -PSM +43.006TETHTGVLR 125 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] -0.3358200896870006 null null 2 524.7867 528.77524981688 ms_run[1]:index=124 null null null null 0.58380,0.52438,0.49959,0.47740,0.82768,0.82780,0.82755,0.66737,0.65260,0.59103 -PSM YHTVNHSEDEVR 126 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.884794716651623 null null 2 743.3352 743.3394818168799 ms_run[1]:index=125 null null null null 0.93470,0.80169,0.92293,0.68049,0.73951,0.86325,0.93716,0.93555,0.93681,0.93724,0.93721,0.93834 -PSM RC+57.021DELTR 127 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.9664741232991219 null null 2 475.22992 475.22962931688 ms_run[1]:index=126 null null null null 0.88668,0.97900,0.97846,0.97710,0.97479,0.97835,0.97884 -PSM RPDQQLQGDGK 128 null null null null [MS, MS:1003281, Casanovo, 4.1.1.dev15+gcedfaa7.d20240625] 0.8267864262064298 null null 2 621.31757 621.31528381688 ms_run[1]:index=127 null null null null 0.90773,0.90631,0.88548,0.90531,0.58918,0.89288,0.61460,0.64761,0.87983,0.87351,0.91032 From cd9bfe5d05e8bf34aedd6ef7047bcdfd31b8a5ac Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 6 Aug 2024 14:03:19 -0700 Subject: [PATCH 27/36] implemen eval mode at model runner level, fix unit test --- casanovo/data/datasets.py | 21 +++------ casanovo/denovo/dataloaders.py | 20 +++------ casanovo/denovo/model.py | 76 +++++++-------------------------- casanovo/denovo/model_runner.py | 44 +++++++++++++++---- tests/test_integration.py | 2 +- tests/unit_tests/test_runner.py | 8 ++-- tests/unit_tests/test_unit.py | 5 +-- 7 files changed, 69 insertions(+), 107 deletions(-) diff --git a/casanovo/data/datasets.py b/casanovo/data/datasets.py index bd3d93af..3917a2c8 100644 --- a/casanovo/data/datasets.py +++ b/casanovo/data/datasets.py @@ -83,11 +83,12 @@ def __getitem__( The unique spectrum identifier, formed by its original peak file and identifier (index or scan number) therein. """ - mz_array, int_array, precursor_mz, precursor_charge = self.index[idx] + mz_array, int_array, precursor_mz, precursor_charge = self.index[idx][ + :4 + ] spectrum = self._process_peaks( mz_array, int_array, precursor_mz, precursor_charge ) - return ( spectrum, precursor_mz, @@ -235,9 +236,7 @@ def __init__( random_state=random_state, ) - def __getitem__( - self, idx: int - ) -> Tuple[torch.Tensor, float, int, Tuple[str, str], str]: + def __getitem__(self, idx: int) -> Tuple[torch.Tensor, float, int, str]: """ Return the annotated MS/MS spectrum with the given index. @@ -254,9 +253,6 @@ def __getitem__( The precursor m/z. precursor_charge : int The precursor charge. - spectrum_id: Tuple[str, str] - The unique spectrum identifier, formed by its original peak file and - identifier (index or scan number) therein. annotation : str The peptide annotation of the spectrum. """ @@ -270,11 +266,4 @@ def __getitem__( spectrum = self._process_peaks( mz_array, int_array, precursor_mz, precursor_charge ) - - return ( - spectrum, - precursor_mz, - precursor_charge, - self.get_spectrum_id(idx), - peptide, - ) + return spectrum, precursor_mz, precursor_charge, peptide diff --git a/casanovo/denovo/dataloaders.py b/casanovo/denovo/dataloaders.py index 9a8b1e32..fe5d6237 100644 --- a/casanovo/denovo/dataloaders.py +++ b/casanovo/denovo/dataloaders.py @@ -175,8 +175,8 @@ def predict_dataloader(self) -> torch.utils.data.DataLoader: def prepare_batch( - batch: List[Tuple[torch.Tensor, float, int, str, Optional[str]]] -) -> Tuple[torch.Tensor, torch.Tensor, np.ndarray, np.ndarray | None]: + batch: List[Tuple[torch.Tensor, float, int, str]] +) -> Tuple[torch.Tensor, torch.Tensor, np.ndarray]: """ Collate MS/MS spectra into a batch. @@ -185,11 +185,10 @@ def prepare_batch( Parameters ---------- - batch : List[Tuple[torch.Tensor, float, int, str, Optional[str]]] + batch : List[Tuple[torch.Tensor, float, int, str]] A batch of data from an AnnotatedSpectrumDataset, consisting of for each spectrum (i) a tensor with the m/z and intensity peak values, (ii), the - precursor m/z, (iii) the precursor charge, (iv) the spectrum identifier, - (v) optionally the peptide sequence annotation + precursor m/z, (iii) the precursor charge, (iv) the spectrum identifier. Returns ------- @@ -202,15 +201,8 @@ def prepare_batch( spectrum_ids : np.ndarray The spectrum identifiers (during de novo sequencing) or peptide sequences (during training). - annotations : np.ndarray | None - The peptide annotations of the spectra if provided by the dataset, - None otherwise """ - batch_list = list(zip(*batch)) - spectra, precursor_mzs, precursor_charges, spectrum_ids = batch_list[0:4] - peptide_sequence = ( - None if len(batch_list) <= 4 else np.asarray(batch_list[4]) - ) + spectra, precursor_mzs, precursor_charges, spectrum_ids = list(zip(*batch)) spectra = torch.nn.utils.rnn.pad_sequence(spectra, batch_first=True) precursor_mzs = torch.tensor(precursor_mzs) precursor_charges = torch.tensor(precursor_charges) @@ -218,4 +210,4 @@ def prepare_batch( precursors = torch.vstack( [precursor_masses, precursor_charges, precursor_mzs] ).T.float() - return spectra, precursors, np.asarray(spectrum_ids), peptide_sequence + return spectra, precursors, np.asarray(spectrum_ids) diff --git a/casanovo/denovo/model.py b/casanovo/denovo/model.py index aae8d925..77df6df5 100644 --- a/casanovo/denovo/model.py +++ b/casanovo/denovo/model.py @@ -748,7 +748,7 @@ def training_step( torch.Tensor The loss of the training step. """ - pred, truth = self._forward_step(batch[0], batch[1], batch[3]) + pred, truth = self._forward_step(*batch) pred = pred[:, :-1, :].reshape(-1, self.decoder.vocab_size + 1) if mode == "train": loss = self.celoss(pred, truth.flatten()) @@ -773,7 +773,7 @@ def validation_step( ---------- batch : Tuple[torch.Tensor, torch.Tensor, List[str]] A batch of (i) MS/MS spectra, (ii) precursor information, (iii) - spectrum identifiers, (iv) peptide sequence annotations + peptide sequences. Returns ------- @@ -781,15 +781,14 @@ def validation_step( The loss of the validation step. """ # Record the loss. - forward_step = self.forward(batch[0], batch[1]) loss = self.training_step(batch, mode="valid") if not self.calculate_precision: - return loss, self._get_predictions(batch, forward_step) + return loss # Calculate and log amino acid and peptide match evaluation metrics from # the predicted peptides. - peptides_pred, peptides_true = [], batch[3] - for spectrum_preds in forward_step: + peptides_pred, peptides_true = [], batch[2] + for spectrum_preds in self.forward(batch[0], batch[1]): for _, _, pred in spectrum_preds: peptides_pred.append(pred) @@ -811,35 +810,26 @@ def validation_step( aa_precision, **log_args, ) - return loss, self._get_predictions(batch, forward_step) + return loss - def _get_predictions( - self, - batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], - forward_res: List[List[Tuple[float, np.ndarray, str]]], + def predict_step( + self, batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], *args ) -> List[Tuple[np.ndarray, float, float, str, float, np.ndarray]]: """ - Extract predictions from model output for a batch of spectra. - - Processes the output from a forward pass of the model to - generate a list of predictions for each spectrum in the batch. + A single prediction step. Parameters ---------- batch : Tuple[torch.Tensor, torch.Tensor, torch.Tensor] - A tuple containing: - - (i) MS/MS spectra data as a torch.Tensor. - - (ii) Precursor information, including charge and m/z values, - - (iii) Spectrum identifiers as a torch.Tensor. - forward_res : List[List[Tuple[float, np.ndarray, str]]] - Output from forward_step + A batch of (i) MS/MS spectra, (ii) precursor information, (iii) + spectrum identifiers as torch Tensors. Returns ------- - List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] - Model predictions for the given batch of spectra containing - spectrum ids, precursor information, peptide sequences as well as - peptide and amino acid-level confidence scores. + predictions: List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] + Model predictions for the given batch of spectra containing spectrum + ids, precursor information, peptide sequences as well as peptide + and amino acid-level confidence scores. """ predictions = [] for ( @@ -851,7 +841,7 @@ def _get_predictions( batch[1][:, 1].cpu().detach().numpy(), batch[1][:, 2].cpu().detach().numpy(), batch[2], - forward_res, + self.forward(batch[0], batch[1]), ): for peptide_score, aa_scores, peptide in spectrum_preds: predictions.append( @@ -867,27 +857,6 @@ def _get_predictions( return predictions - def predict_step( - self, batch: Tuple[torch.Tensor, torch.Tensor, torch.Tensor], *args - ) -> List[Tuple[np.ndarray, float, float, str, float, np.ndarray]]: - """ - A single prediction step. - - Parameters - ---------- - batch : Tuple[torch.Tensor, torch.Tensor, torch.Tensor] - A batch of (i) MS/MS spectra, (ii) precursor information, (iii) - spectrum identifiers as torch Tensors. - - Returns - ------- - predictions: List[Tuple[np.ndarray, float, float, str, float, np.ndarray]] - Model predictions for the given batch of spectra containing spectrum - ids, precursor information, peptide sequences as well as peptide - and amino acid-level confidence scores. - """ - return self._get_predictions(batch, self.forward(batch[0], batch[1])) - def on_train_epoch_end(self) -> None: """ Log the training loss at the end of each epoch. @@ -956,19 +925,6 @@ def on_predict_batch_end( ), ) - def on_validation_batch_end( - self, - outputs: Tuple[ - torch.Tensor, List[Tuple[np.ndarray, List[str], torch.Tensor]] - ], - *args, - ) -> None: - """ - Write the predicted peptide sequences and amino acid scores to the - output file. - """ - self.on_predict_batch_end(outputs[1]) - def _log_history(self) -> None: """ Write log to console, if requested. diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 523a4e60..727cf1f9 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -10,6 +10,7 @@ from pathlib import Path from typing import Iterable, List, Optional, Union +import depthcharge.masses import lightning.pytorch as pl import numpy as np import torch @@ -20,6 +21,7 @@ from ..config import Config from ..data import ms_io from ..denovo.dataloaders import DeNovoDataModule +from ..denovo.evaluate import aa_match_batch, aa_match_metrics from ..denovo.model import Spec2Pep @@ -118,8 +120,35 @@ def train( self.loaders.val_dataloader(), ) + def log_metrics(self, test_index: AnnotatedSpectrumIndex) -> None: + """Log pep_precision and aa_precision + + Calculate and log peptide precision and amino acid precision + based off of model predictions and spectrum annotations + + Parameters + ---------- + test_index : AnnotatedSpectrumIndex + Index containing the annotated spectra used to generate model + predictions + """ + model_output = [psm[0] for psm in self.writer.psms] + spectrum_annotations = [ + test_index[i][4] for i in range(test_index.n_spectra) + ] + aa_precision, _, pep_precision = aa_match_metrics( + *aa_match_batch( + spectrum_annotations, + model_output, + depthcharge.masses.PeptideMass().masses, + ) + ) + + logger.info("Peptide Precision: %f", pep_precision) + logger.info("Amino Acid Precision: %f", aa_precision) + def predict( - self, peak_path: Iterable[str], output: str, evaluate=False + self, peak_path: Iterable[str], output: str, evaluate: bool = False ) -> None: """Predict peptide sequences with a trained Casanovo model. @@ -132,7 +161,7 @@ def predict( The path with the MS data files for predicting peptide sequences. output : str Where should the output be saved? - evaluate: str + evaluate: bool whether to run model evaluation in addition to inference Note: peak_path most point to annotated MS data files when running model evaluation. Files that are not an annotated @@ -153,17 +182,14 @@ def predict( self.initialize_model(train=False) self.model.out_writer = self.writer - test_index = self._get_index( - peak_path, evaluate, "evaluation" if evaluate else "" - ) + test_index = self._get_index(peak_path, evaluate, "") self.writer.set_ms_run(test_index.ms_files) self.initialize_data_module(test_index=test_index) - self.loaders.setup(stage="test", annotated=evaluate) + self.loaders.setup(stage="test", annotated=False) + self.trainer.predict(self.model, self.loaders.test_dataloader()) if evaluate: - self.trainer.validate(self.model, self.loaders.test_dataloader()) - else: - self.trainer.predict(self.model, self.loaders.test_dataloader()) + self.log_metrics(test_index) def initialize_trainer(self, train: bool) -> None: """Initialize the lightning Trainer. diff --git a/tests/test_integration.py b/tests/test_integration.py index 54b09741..43073580 100644 --- a/tests/test_integration.py +++ b/tests/test_integration.py @@ -41,7 +41,7 @@ def test_train_and_run( assert model_file.exists() assert best_model.exists() - # Try predicting: + # Finally try predicting: output_filename = tmp_path / "test.mztab" predict_args = [ "sequence", diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index b64254bc..356ba552 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -56,7 +56,7 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): config.max_epochs = 1 config.n_layers = 1 ckpt = tmp_path / "test.ckpt" - output_file = tmp_path / "out" + mztab = tmp_path / "test.mztab" with ModelRunner(config=config) as runner: runner.train([mgf_small], [mgf_small]) @@ -84,7 +84,7 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): with torch.device("meta"): with ModelRunner(other_config, model_filename=str(ckpt)) as runner: with pytest.raises(NotImplementedError) as err: - runner.predict([mgf_small], output_file, evaluate=True) + runner.predict([mgf_small], mztab) assert "meta tensor; no data!" in str(err.value) @@ -96,11 +96,11 @@ def test_save_and_load_weights(tmp_path, mgf_small, tiny_config): # Shouldn't work: with ModelRunner(other_config, model_filename=str(ckpt)) as runner: with pytest.raises(RuntimeError): - runner.predict([mgf_small], output_file, evaluate=True) + runner.predict([mgf_small], mztab) # Should work: with ModelRunner(config=config, model_filename=str(ckpt)) as runner: - runner.predict([mgf_small], output_file, evaluate=True) + runner.predict([mgf_small], mztab) def test_save_and_load_weights_deprecated(tmp_path, mgf_small, tiny_config): diff --git a/tests/unit_tests/test_unit.py b/tests/unit_tests/test_unit.py index b928ab4e..120e341a 100644 --- a/tests/unit_tests/test_unit.py +++ b/tests/unit_tests/test_unit.py @@ -895,11 +895,10 @@ def test_train_val_step_functions(): spectra = torch.zeros(1, 5, 2) precursors = torch.tensor([[469.25364, 2.0, 235.63410]]) peptides = ["PEPK"] - spectrum_id = "foobar" - batch = (spectra, precursors, spectrum_id, peptides) + batch = (spectra, precursors, peptides) train_step_loss = model.training_step(batch) - val_step_loss, _ = model.validation_step(batch) + val_step_loss = model.validation_step(batch) # Check if valid loss value returned assert train_step_loss > 0 From 5cb3e214e00e213a58e27787441a730e9e584e24 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 6 Aug 2024 14:22:23 -0700 Subject: [PATCH 28/36] CLI documentation --- casanovo/casanovo.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index 98597162..48ed7c79 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -133,7 +133,12 @@ def main() -> None: "-e", is_flag=True, default=False, - help="Run in evaluation mode.", + help=""" + Run in evaluation mode. When this flag is set the peptide and amino + acid precision will be calculate and logged at the end of the sequencing + run. All input files must be annotated MGF files if running in evaluation + mode. + """, ) def sequence( peak_path: Tuple[str], @@ -146,7 +151,8 @@ def sequence( """De novo sequence peptides from tandem mass spectra. PEAK_PATH must be one or more mzML, mzXML, or MGF files from which - to sequence peptides. + to sequence peptides. If evaluate is set to true peak_path must be + one or more annotated MGF file. """ output = setup_logging(output, verbosity) config, model = setup_model(model, config, output, False) From 0bb617d2fc8a5ad031bc8b2fc0fc727328d16f24 Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Tue, 6 Aug 2024 08:47:53 +0200 Subject: [PATCH 29/36] Bug report template (#360) * bug report template * punctuation, hardware description item * Restrict NumPy to pre-2.0 (#344) * Restrict NumPy to pre-2.0 * Update changelog * Update paper reference (#361) --------- Co-authored-by: Lilferrit --- .github/ISSUE_TEMPLATE/bug_report_template.md | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/bug_report_template.md diff --git a/.github/ISSUE_TEMPLATE/bug_report_template.md b/.github/ISSUE_TEMPLATE/bug_report_template.md new file mode 100644 index 00000000..cf4c487c --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report_template.md @@ -0,0 +1,55 @@ +--- +name: Bug Report +about: Submit a Casanovo Bug Report +labels: bug +--- + +## Describe the Issue +A clear and concise description of what the issue/bug is. + +## Steps To Reproduce +Steps to reproduce the incorrect behavior. + +## Expected Behavior +A clear and concise description of what you expected to happen. + +## Terminal Output (If Applicable) +Provide any applicable console output in between the tick marks below. + +``` + +``` + +## Environment: +- OS: [e.g. Windows 11, Windows 10, macOS 14, Ubuntu 24.04] +- Casanovo Version: [e.g. 4.2.1] +- Hardware Used (CPU or GPU, if GPU also GPU model and CUDA version): [e.g. GPU: NVIDIA GeForce RTX 2070, CUDA Version: 12.5] + +### Checking GPU Version + +The GPU model can be checked by typing `nvidia-smi` into a terminal/console window. +An example of how to use this command is shown below. +In this case, the CUDA version is 12.5 and the GPU model is GeForce RTX 2070. + + +``` +(casanovo_env) C:\Users\\OneDrive\Documents\casanovo>nvidia-smi +Fri Aug 2 12:34:57 2024 ++-----------------------------------------------------------------------------------------+ +| NVIDIA-SMI 555.99 Driver Version: 555.99 CUDA Version: 12.5 | +|-----------------------------------------+------------------------+----------------------+ +| GPU Name Driver-Model | Bus-Id Disp.A | Volatile Uncorr. ECC | +| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. | +| | | MIG M. | +|=========================================+========================+======================| +| 0 NVIDIA GeForce RTX 2070 ... WDDM | 00000000:01:00.0 On | N/A | +| N/A 60C P8 16W / 90W | 1059MiB / 8192MiB | 0% Default | +| | | N/A | ++-----------------------------------------+------------------------+----------------------+ +``` + +## Additional Context +Add any other context about the problem here. + +## Attach Files +Please attach all input files used and the full Casanovo log file. From 7be64ed380d2443854430b32b67ab261a67f81b1 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Wed, 7 Aug 2024 14:26:59 -0700 Subject: [PATCH 30/36] requested changes --- casanovo/casanovo.py | 2 +- casanovo/denovo/model_runner.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index 48ed7c79..33c3b332 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -151,7 +151,7 @@ def sequence( """De novo sequence peptides from tandem mass spectra. PEAK_PATH must be one or more mzML, mzXML, or MGF files from which - to sequence peptides. If evaluate is set to true peak_path must be + to sequence peptides. If evaluate is set to True PEAK_PATH must be one or more annotated MGF file. """ output = setup_logging(output, verbosity) diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 727cf1f9..5652d4b5 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -121,7 +121,7 @@ def train( ) def log_metrics(self, test_index: AnnotatedSpectrumIndex) -> None: - """Log pep_precision and aa_precision + """Log peptide precision and amino acid precision Calculate and log peptide precision and amino acid precision based off of model predictions and spectrum annotations @@ -144,8 +144,8 @@ def log_metrics(self, test_index: AnnotatedSpectrumIndex) -> None: ) ) - logger.info("Peptide Precision: %f", pep_precision) - logger.info("Amino Acid Precision: %f", aa_precision) + logger.info("Peptide Precision: %.2f%%", 100 * pep_precision) + logger.info("Amino Acid Precision: %.2f%%", 100 * aa_precision) def predict( self, peak_path: Iterable[str], output: str, evaluate: bool = False From b5862b5fe545bae6dfe38aa226b4062e054cf30a Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Wed, 7 Aug 2024 16:07:36 -0700 Subject: [PATCH 31/36] evaluation test cases --- tests/conftest.py | 26 ++++++++++++++++++++++---- tests/unit_tests/test_runner.py | 31 +++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+), 4 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 54c8d03c..bff6b011 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -15,7 +15,15 @@ def mgf_small(tmp_path): return _create_mgf(peptides, mgf_file) -def _create_mgf(peptides, mgf_file, random_state=42): +@pytest.fixture +def mgf_small_unannotated(tmp_path): + """An MGF file with 2 unannotated spectra.""" + peptides = ["LESLIEK", "PEPTIDEK"] + mgf_file = tmp_path / "small_unannotated.mgf" + return _create_mgf(peptides, mgf_file, annotate=False) + + +def _create_mgf(peptides, mgf_file, random_state=42, annotate=True): """ Create a fake MGF file from one or more peptides. @@ -27,20 +35,25 @@ def _create_mgf(peptides, mgf_file, random_state=42): The MGF file to create. random_state : int or numpy.random.Generator, optional The random seed. The charge states are chosen to be 2 or 3 randomly. + annotate: bool, optional + Whether to add peptide annotations to mgf file Returns ------- mgf_file : Path """ rng = np.random.default_rng(random_state) - entries = [_create_mgf_entry(p, rng.choice([2, 3])) for p in peptides] + entries = [ + _create_mgf_entry(p, rng.choice([2, 3]), annotate=annotate) + for p in peptides + ] with mgf_file.open("w+") as mgf_ref: mgf_ref.write("\n".join(entries)) return mgf_file -def _create_mgf_entry(peptide, charge=2): +def _create_mgf_entry(peptide, charge=2, annotate=True): """ Create a MassIVE-KB style MGF entry for a single PSM. @@ -50,6 +63,8 @@ def _create_mgf_entry(peptide, charge=2): A peptide sequence. charge : int, optional The peptide charge state. + annotate: bool, optional + Whether to add peptide annotation to entry Returns ------- @@ -62,12 +77,15 @@ def _create_mgf_entry(peptide, charge=2): mgf = [ "BEGIN IONS", - f"SEQ={peptide}", f"PEPMASS={precursor_mz}", f"CHARGE={charge}+", f"{frags}", "END IONS", ] + + if annotate: + mgf.insert(1, f"SEQ={peptide}") + return "\n".join(mgf) diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index 356ba552..1ed6b968 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -175,3 +175,34 @@ def test_save_final_model(tmp_path, mgf_small, tiny_config): assert model_file.exists() assert validation_file.exists() + + +def test_evaluate( + tmp_path, mgf_small, mzml_small, mgf_small_unannotated, tiny_config +): + """Test model evaluation during sequencing""" + # Train tiny model + config = Config(tiny_config) + config.max_epochs = 1 + model_file = tmp_path / "epoch=0-step=1.ckpt" + with ModelRunner(config) as runner: + runner.train([mgf_small], [mgf_small]) + + assert model_file.is_file() + + # Test evaluation with annotated peak file + result_file = tmp_path / "result.mzTab" + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mgf_small], result_file, evaluate=True) + + assert result_file.is_file() + result_file.unlink() + + # Test evaluation with unannotated peak files + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mgf_small_unannotated], result_file, evaluate=True) + + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mzml_small], result_file, evaluate=True) + + assert not result_file.is_file() From d20494c1d8e056dfc2e417bc34806ad77844d3b7 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Thu, 8 Aug 2024 13:44:00 -0700 Subject: [PATCH 32/36] file warnings, evaluation tests --- casanovo/denovo/model_runner.py | 22 ++++++++++++++++++--- tests/unit_tests/test_runner.py | 35 ++++++++++++++++++++++++++++----- 2 files changed, 49 insertions(+), 8 deletions(-) diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 5652d4b5..a4624b50 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -417,9 +417,15 @@ def _get_index( else: index_fname = Path(self.tmp_dir.name) / f"{uuid.uuid4().hex}.hdf5" - Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex - valid_charge = np.arange(1, self.config.max_charge + 1) - return Index(index_fname, filenames, valid_charge=valid_charge) + try: + Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex + valid_charge = np.arange(1, self.config.max_charge + 1) + return Index(index_fname, filenames, valid_charge=valid_charge) + except TypeError: + raise ValueError( + "MGF peak files must be annotated when constructing " + "annotated spectrum indices." + ) def _get_strategy(self) -> Union[str, DDPStrategy]: """Get the strategy for the Trainer. @@ -472,5 +478,15 @@ def _get_peak_filenames( for fname in glob.glob(path, recursive=True): if Path(fname).suffix.lower() in supported_ext: found_files.add(fname) + else: + warnings.warn( + f"Ignoring unsupported peak file: {fname}", RuntimeWarning + ) + + if len(found_files) == 0: + warnings.warn( + f"No supported peak files found under path(s): {list(paths)}", + RuntimeWarning, + ) return sorted(list(found_files)) diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index 1ed6b968..52f4b555 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -199,10 +199,35 @@ def test_evaluate( result_file.unlink() # Test evaluation with unannotated peak files - with ModelRunner(config, model_filename=str(model_file)) as runner: - runner.predict([mgf_small_unannotated], result_file, evaluate=True) + with pytest.raises(FileNotFoundError): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mzml_small], result_file, evaluate=True) - with ModelRunner(config, model_filename=str(model_file)) as runner: - runner.predict([mzml_small], result_file, evaluate=True) + with pytest.raises(ValueError): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mgf_small_unannotated], result_file, evaluate=True) + + with pytest.raises(ValueError): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict( + [mgf_small_unannotated, mzml_small], result_file, evaluate=True + ) + + # Test mix of annotated an unannotated peak files + with pytest.warns(RuntimeWarning): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict([mgf_small, mzml_small], result_file, evaluate=True) - assert not result_file.is_file() + with pytest.raises(ValueError): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict( + [mgf_small, mgf_small_unannotated], result_file, evaluate=True + ) + + with pytest.raises(ValueError): + with ModelRunner(config, model_filename=str(model_file)) as runner: + runner.predict( + [mgf_small, mgf_small_unannotated, mzml_small], + result_file, + evaluate=True, + ) From 9647321a5905989bd931823a980cf4321cb8ac6c Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Thu, 8 Aug 2024 15:54:35 -0700 Subject: [PATCH 33/36] fixed ubuntu specific test case bug --- tests/unit_tests/test_runner.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index 52f4b555..7ce3660a 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -191,7 +191,7 @@ def test_evaluate( assert model_file.is_file() # Test evaluation with annotated peak file - result_file = tmp_path / "result.mzTab" + result_file = tmp_path / "result.mztab" with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mgf_small], result_file, evaluate=True) From c4cd147a355ba02015c7b3bfe692cea8eff0e7ff Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Fri, 9 Aug 2024 13:30:48 -0700 Subject: [PATCH 34/36] verify annotated mgf files --- casanovo/casanovo.py | 2 +- casanovo/denovo/model_runner.py | 55 +++++++++++++++++++++++++++------ tests/unit_tests/test_runner.py | 28 ++++++++++++++--- 3 files changed, 69 insertions(+), 16 deletions(-) diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index 33c3b332..0c220ddb 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -135,7 +135,7 @@ def main() -> None: default=False, help=""" Run in evaluation mode. When this flag is set the peptide and amino - acid precision will be calculate and logged at the end of the sequencing + acid precision will be calculated and logged at the end of the sequencing run. All input files must be annotated MGF files if running in evaluation mode. """, diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index a4624b50..40e3a505 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -8,7 +8,7 @@ import uuid import warnings from pathlib import Path -from typing import Iterable, List, Optional, Union +from typing import Iterable, List, Optional, Union, TextIO import depthcharge.masses import lightning.pytorch as pl @@ -401,6 +401,21 @@ def _get_index( msg = msg.strip() filenames = _get_peak_filenames(peak_path, ext) + if annotated: + # Filter unannotated MGF files to avoid Depth Charge exception + filtered_fnames = list() + for fname in filenames: + if Path( + fname + ).suffix.lower() == ".mgf" and not _mgf_is_annotated(fname): + warnings.warn( + f"Ignoring unannotated MGF peak file: {fname}", + RuntimeWarning, + ) + else: + filtered_fnames.append(fname) + filenames = filtered_fnames + if not filenames: not_found_err = f"Cound not find {msg} peak files" logger.error(not_found_err + " from %s", peak_path) @@ -417,15 +432,9 @@ def _get_index( else: index_fname = Path(self.tmp_dir.name) / f"{uuid.uuid4().hex}.hdf5" - try: - Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex - valid_charge = np.arange(1, self.config.max_charge + 1) - return Index(index_fname, filenames, valid_charge=valid_charge) - except TypeError: - raise ValueError( - "MGF peak files must be annotated when constructing " - "annotated spectrum indices." - ) + Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex + valid_charge = np.arange(1, self.config.max_charge + 1) + return Index(index_fname, filenames, valid_charge=valid_charge) def _get_strategy(self) -> Union[str, DDPStrategy]: """Get the strategy for the Trainer. @@ -450,6 +459,32 @@ def _get_strategy(self) -> Union[str, DDPStrategy]: return "auto" +def _mgf_is_annotated(mgf_path: TextIO) -> bool: + """Check whether MGF file is annotated + + Parameters + ---------- + mgf_path : TextIO + MGF peak file to check + + Returns + ------- + bool + Whether MGF peak file is annotated + """ + num_spectra = 0 + num_annotations = 0 + + with open(mgf_path) as f: + for curr_line in f: + if curr_line.startswith("BEGIN IONS"): + num_spectra += 1 + elif curr_line.startswith("SEQ="): + num_annotations += 1 + + return num_spectra == num_annotations + + def _get_peak_filenames( paths: Iterable[str], supported_ext: Iterable[str] ) -> List[str]: diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index 7ce3660a..279b1710 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -6,7 +6,7 @@ import torch from casanovo.config import Config -from casanovo.denovo.model_runner import ModelRunner +from casanovo.denovo.model_runner import ModelRunner, _mgf_is_annotated def test_initialize_model(tmp_path, mgf_small): @@ -203,31 +203,49 @@ def test_evaluate( with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mzml_small], result_file, evaluate=True) - with pytest.raises(ValueError): + with pytest.raises(FileNotFoundError): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mgf_small_unannotated], result_file, evaluate=True) - with pytest.raises(ValueError): + with pytest.raises(FileNotFoundError): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small_unannotated, mzml_small], result_file, evaluate=True ) + # MzTab with just metadata is written in the case of FileNotFound + # early exit + result_file.unlink() + # Test mix of annotated an unannotated peak files with pytest.warns(RuntimeWarning): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mgf_small, mzml_small], result_file, evaluate=True) - with pytest.raises(ValueError): + assert result_file.is_file() + result_file.unlink() + + with pytest.warns(RuntimeWarning): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small, mgf_small_unannotated], result_file, evaluate=True ) - with pytest.raises(ValueError): + assert result_file.is_file() + result_file.unlink() + + with pytest.warns(RuntimeWarning): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small, mgf_small_unannotated, mzml_small], result_file, evaluate=True, ) + + assert result_file.is_file() + result_file.unlink() + + +def test_mgf_is_annotated(mgf_small, mgf_small_unannotated): + assert _mgf_is_annotated(mgf_small) + assert not _mgf_is_annotated(mgf_small_unannotated) From 695c739ae1368c569dee00e0e4b2262e535b00a6 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Wed, 14 Aug 2024 14:35:46 -0700 Subject: [PATCH 35/36] AnnotatedSpectrumIndex type error --- casanovo/denovo/model_runner.py | 14 +++++++++++++- tests/unit_tests/test_runner.py | 19 ++++++++++--------- 2 files changed, 23 insertions(+), 10 deletions(-) diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index 713760a4..c101af4c 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -419,7 +419,19 @@ def _get_index( Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex valid_charge = np.arange(1, self.config.max_charge + 1) - return Index(index_fname, filenames, valid_charge=valid_charge) + + try: + return Index(index_fname, filenames, valid_charge=valid_charge) + except TypeError as e: + if Index == AnnotatedSpectrumIndex: + raise TypeError( + "Error creating annotated spectrum index. " + "This may be the result of having an unannotated MGF file " + "present in the validation peak file path list.\n" + f"Original error message: {e}" + ) + + raise e def _get_strategy(self) -> Union[str, DDPStrategy]: """Get the strategy for the Trainer. diff --git a/tests/unit_tests/test_runner.py b/tests/unit_tests/test_runner.py index c10f035f..db21725a 100644 --- a/tests/unit_tests/test_runner.py +++ b/tests/unit_tests/test_runner.py @@ -198,20 +198,21 @@ def test_evaluate( assert result_file.is_file() result_file.unlink() - # Test evaluation with unannotated peak files - # NOTE: Depth Charge raises a TypeError exception when an unannotated - # peak file is in the peak file list when initializing a - # AnnotatedSpectrumIndex - # TODO: Reexamine after Depth Charge v0.4 release + exception_string = ( + "Error creating annotated spectrum index. " + "This may be the result of having an unannotated MGF file " + "present in the validation peak file path list.\n" + ) + with pytest.raises(FileNotFoundError): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mzml_small], result_file, evaluate=True) - with pytest.raises(TypeError): + with pytest.raises(TypeError, match=exception_string): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict([mgf_small_unannotated], result_file, evaluate=True) - with pytest.raises(TypeError): + with pytest.raises(TypeError, match=exception_string): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small_unannotated, mzml_small], result_file, evaluate=True @@ -230,7 +231,7 @@ def test_evaluate( assert result_file.is_file() result_file.unlink() - with pytest.raises(TypeError): + with pytest.raises(TypeError, match=exception_string): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small, mgf_small_unannotated], result_file, evaluate=True @@ -239,7 +240,7 @@ def test_evaluate( assert result_file.is_file() result_file.unlink() - with pytest.raises(TypeError): + with pytest.raises(TypeError, match=exception_string): with ModelRunner(config, model_filename=str(model_file)) as runner: runner.predict( [mgf_small, mgf_small_unannotated, mzml_small], From 2d882b7d6fd8c3430f7f2f1f04e0363c3d2e3880 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 20 Aug 2024 15:53:06 -0700 Subject: [PATCH 36/36] requested changes, changelog entry --- CHANGELOG.md | 4 ++++ casanovo/denovo/model_runner.py | 5 ++++- tests/test_integration.py | 8 ++++---- 3 files changed, 12 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c4559d33..12a92e38 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - During training, model checkpoints will be saved at the end of each training epoch in addition to the checkpoints saved at the end of every validation run. - Besides as a local file, model weights can be specified from a URL. Upon initial download, the weights file is cached for future re-use. +### Changed + +- Removed the `evaluate` sub-command, and all model evaluation functionality has been moved to the `sequence` command using the new `--evaluate` flag. + ### Fixed - Precursor charges are exported as integers instead of floats in the mzTab output file, in compliance with the mzTab specification. diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py index c101af4c..b88c5542 100644 --- a/casanovo/denovo/model_runner.py +++ b/casanovo/denovo/model_runner.py @@ -424,13 +424,16 @@ def _get_index( return Index(index_fname, filenames, valid_charge=valid_charge) except TypeError as e: if Index == AnnotatedSpectrumIndex: - raise TypeError( + error_msg = ( "Error creating annotated spectrum index. " "This may be the result of having an unannotated MGF file " "present in the validation peak file path list.\n" f"Original error message: {e}" ) + logger.error(error_msg) + raise TypeError(error_msg) + raise e def _get_strategy(self) -> Union[str, DDPStrategy]: diff --git a/tests/test_integration.py b/tests/test_integration.py index 43073580..47cee936 100644 --- a/tests/test_integration.py +++ b/tests/test_integration.py @@ -97,10 +97,10 @@ def test_train_and_run( assert output_filename.is_file() mztab = pyteomics.mztab.MzTab(str(output_filename)) - # Verify that both input peak files are listed in the metadata. - for i, filename in enumerate(["small.mgf"], 1): - assert f"ms_run[{i}]-location" in mztab.metadata - assert mztab.metadata[f"ms_run[{i}]-location"].endswith(filename) + filename = "small.mgf" + # Verify that the input annotated peak file is listed in the metadata. + assert f"ms_run[1]-location" in mztab.metadata + assert mztab.metadata[f"ms_run[1]-location"].endswith(filename) # Verify that the spectrum predictions are correct # and indexed according to the peak input file type.