MQ files and new nan

proteobench/io/params/__init__.py

@@ -97,7 +97,7 @@ def __init__(
         for key, value in kwargs.items():
             print(key, value)
             if hasattr(self, key) and value == "None":
-                setattr(self, key, np.NaN)
+                setattr(self, key, np.nan)
             elif hasattr(self, key):
                 setattr(self, key, value)
 
@@ -109,11 +109,11 @@ def __repr__(self):
 
     def fill_none(self):
         """
-        Fill all None values with np.NaN
+        Fill all None values with np.nan
         """
         for key, value in self.__dict__.items():
             if value == "None":
-                setattr(self, key, np.NaN)
+                setattr(self, key, np.nan)
 
 
 # Automatically initialize from fields.json if run directly

test/params/mqpar1.5.3.30_MBR_sel.json

@@ -1,8 +1,8 @@
 {
-    "software_name": null,
+    "software_name": NaN,
     "software_version": "1.5.3.30",
     "search_engine": "Andromeda",
-    "search_engine_version": null,
+    "search_engine_version": "1.0",
     "ident_fdr_psm": null,
     "ident_fdr_peptide": 0.01,
     "ident_fdr_protein": 0.01,
@@ -18,10 +18,7 @@
     "max_mods": 5,
     "min_precursor_charge": null,
     "max_precursor_charge": 7,
-    "scan_window": null,
-    "quantification_method": null,
-    "second_pass": null,
-    "protein_inference": null,
-    "predictors_library": null,
-    "abundance_normalization_ions": null
+    "quantification_method": NaN,
+    "protein_inference": NaN,
+    "abundance_normalization_ions": NaN
 }

test/params/mqpar_MQ1.6.3.3_MBR_sel.json

@@ -1,8 +1,8 @@
 {
-    "software_name": null,
+    "software_name": NaN,
     "software_version": "1.6.3.3",
     "search_engine": "Andromeda",
-    "search_engine_version": null,
+    "search_engine_version": "1.0",
     "ident_fdr_psm": null,
     "ident_fdr_peptide": 0.01,
     "ident_fdr_protein": 0.01,
@@ -18,10 +18,7 @@
     "max_mods": 5,
     "min_precursor_charge": null,
     "max_precursor_charge": 7,
-    "scan_window": null,
-    "quantification_method": null,
-    "second_pass": null,
-    "protein_inference": null,
-    "predictors_library": null,
-    "abundance_normalization_ions": null
+    "quantification_method": NaN,
+    "protein_inference": NaN,
+    "abundance_normalization_ions": NaN
 }

test/params/mqpar_MQ2.1.3.0_noMBR_sel.json

@@ -1,8 +1,8 @@
 {
-    "software_name": null,
+    "software_name": NaN,
     "software_version": "2.1.3.0",
     "search_engine": "Andromeda",
-    "search_engine_version": null,
+    "search_engine_version": "1.0",
     "ident_fdr_psm": null,
     "ident_fdr_peptide": 0.01,
     "ident_fdr_protein": 0.01,
@@ -18,10 +18,7 @@
     "max_mods": 5,
     "min_precursor_charge": null,
     "max_precursor_charge": 7,
-    "scan_window": null,
-    "quantification_method": null,
-    "second_pass": null,
-    "protein_inference": null,
-    "predictors_library": null,
-    "abundance_normalization_ions": null
+    "quantification_method": NaN,
+    "protein_inference": NaN,
+    "abundance_normalization_ions": NaN
 }

test/params/mqpar_mq2.6.2.0_1mc_MBR_sel.json

@@ -1,8 +1,8 @@
 {
-    "software_name": null,
+    "software_name": NaN,
     "software_version": "2.6.2.0",
     "search_engine": "Andromeda",
-    "search_engine_version": null,
+    "search_engine_version": "1.0",
     "ident_fdr_psm": null,
     "ident_fdr_peptide": 0.01,
     "ident_fdr_protein": 0.01,
@@ -18,10 +18,7 @@
     "max_mods": 5,
     "min_precursor_charge": null,
     "max_precursor_charge": 7,
-    "scan_window": null,
-    "quantification_method": null,
-    "second_pass": null,
-    "protein_inference": null,
-    "predictors_library": null,
-    "abundance_normalization_ions": null
+    "quantification_method": NaN,
+    "protein_inference": NaN,
+    "abundance_normalization_ions": NaN
 }