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tcrmodel.py
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from flask import Flask, g, render_template, request, redirect, url_for
from flask import json
import os
import paramiko
import string, datetime, random
import subprocess
import commands
import json
import glob
import shutil
import zipfile
from werkzeug.utils import secure_filename
from TCR_functions import *
import sys
import pwd
import grp
import re
import gzip
app = Flask(__name__)
tcrdata = {}
rundir = "tcrmodel_runs"
#Works if rundirpath is one directory down the app (tcrmodel) folder
rundir_path = os.path.abspath(os.path.join(app.root_path, '..', rundir))
#rundir server path
rundir_spath = "/"+rundir
#template db path for pdb and seq
tmplt_db_pdb = "/www/cgi-bin/rosetta/Rosetta/main/database/additional_protocol_data/tcr/pdb/"
tmplt_db_seq = "/www/cgi-bin/rosetta/Rosetta/main/database/additional_protocol_data/tcr/seq/"
tmplt_db_tcrpmhc = "/www/cgi-bin/rosetta/Rosetta/main/database/additional_protocol_data/tcr/tcrpmhc/"
tcrdata['rundir_spath'] = rundir_spath
def get_unique_name(basename):
random_tag = ''.join(random.SystemRandom().choice(string.ascii_uppercase + string.digits) for _ in range(3))
datetime_tag = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
uniquedirname = "_".join([("".join([basename, random_tag])), datetime_tag])
return uniquedirname
def create_and_cd_to_unique_dir(basename):
uniquedirname = get_unique_name(basename)
rundir = os.path.join(rundir_path,uniquedirname)
if not os.path.exists(rundir):
os.makedirs(rundir)
os.chmod(rundir, 0777)
os.chdir(rundir)
return uniquedirname
def get_core_binding_pepseq(pseq):
#subprocess.call(["/www/cgi-bin/netMHCIIpan-4.1/netMHCIIpan -inptype 1 -f ", pepfile], stdout=outfile)
pepfile = "inpepseq.txt"
with open(pepfile, 'w') as pfile:
pfile.write(pseq)
commandline = "/www/cgi-bin/netMHCIIpan-4.1/netMHCIIpan -inptype 1 -f " + pepfile
p = subprocess.Popen(commandline, shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out,err = p.communicate()
for line in out.splitlines():
#skip blank lines, line start with #, - , Pos, Number
if len(line.strip()) == 0 :
continue
if line.startswith("#"):
continue
if line.startswith("-"):
continue
if line.startswith(" Pos"):
continue
if line.startswith("Number"):
continue
core_pseq = line.split()[4]
return core_pseq
def find_templates(inseq, multidb, tag1, tag2, inp_sc_mat=None, pdb_blacklist=None):
tmplt = score_alignment_from_fasta_files_list( inseq, multidb, None, pdb_blacklist )
if all(tmplt):
tcrdata[tag1+'_tmplt_id'] = str(tmplt[1].id)
tcrdata[tag1+'_tmplt_pdb'] = str(tmplt[1].id)[:6].upper()
tcrdata[tag1+'_tmplt_pdbid'] = str(tmplt[1].id)[:4].upper()
tcrdata[tag1+'_tmplt_pdb_chain'] = str(tmplt[1].id)[5:6].upper()
tcrdata[tag1+'_tmplt_seq'] = str(tmplt[1].seq)
else:
errormsg = "No Template found for TCR "+tag2+" segment"
return render_template("error.html", errormsg=errormsg)
def submit_job_on_cluster(uniquejobid,jobscriptfile,ig_file):
HOST="cluster.ibbr.umd.edu"
USER="tcrmodel"
PASSWD="o8!St1Jfqx5xo=x^8FXv%$_sn4W#BO"
remote_dir = "/home/gowthamanr/TCRmodeller/"
remote_location = os.path.join(remote_dir, uniquejobid)
ssh_client = paramiko.SSHClient()
ssh_client.load_system_host_keys()
ssh_client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
ssh_client.connect(HOST, username=USER, password=PASSWD)
sftp = ssh_client.open_sftp()
parent = os.path.join(rundir_path, uniquejobid)
sftp.mkdir(remote_location)
sftp.chdir(remote_location)
sftp.put(jobscriptfile, jobscriptfile)
sftp.put(os.path.join(parent, jobscriptfile), os.path.join(remote_location, jobscriptfile))
ignore_file = os.path.join(parent, ig_file)
if os.path.isfile( ignore_file ):
sftp.put(ignore_file, os.path.join(remote_location, ig_file))
command = "cd %s && sbatch %s" % (remote_location, jobscriptfile)
ssh_stdin, ssh_stdout, ssh_stderr = ssh_client.exec_command(command)
return
def submit_batchjob_on_cluster(uniquejobid,jobscriptfile,ig_file):
HOST="cluster.ibbr.umd.edu"
USER="tcrmodel"
PASSWD="o8!St1Jfqx5xo=x^8FXv%$_sn4W#BO"
remote_dir = "/home/gowthamanr/TCRmodeller/"
remote_location = os.path.join(remote_dir, uniquejobid)
ssh_client = paramiko.SSHClient()
ssh_client.load_system_host_keys()
ssh_client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
ssh_client.connect(HOST, username=USER, password=PASSWD)
sftp = ssh_client.open_sftp()
parent = os.path.join(rundir_path, uniquejobid)
for dirpath, dirnames, filenames in os.walk(parent):
remote_path = os.path.join(remote_location, dirpath[len(parent)+1:])
sftp.mkdir(remote_path)
for filename in filenames:
sftp.put(os.path.join(dirpath, filename), os.path.join(remote_path, filename))
command = "cd %s && csh %s" % (remote_location, jobscriptfile)
ssh_stdin, ssh_stdout, ssh_stderr = ssh_client.exec_command(command)
return
def get_seq_from_genename(gene, trfile):
#(cleanup genenames: Ex. TRBV06-05 to TRBV6-5)
gene = re.sub('-0','-',gene)
gene = re.sub('TRAV0','TRAV',gene)
gene = re.sub('TRAJ0','TRAJ',gene)
gene = re.sub('TRBV0','TRBV',gene)
gene = re.sub('TRBJ0','TRBJ',gene)
trseq = ''
if trfile:
with open(trfile, 'r') as f:
trfiledata = json.loads(f.read());
Found = False
for item in trfiledata:
if item.get('allele_name') == gene:
trseq = item.get('seq')
Found = True
break;
if not Found:
for item in trfiledata:
if item.get('gene_name') == gene:
trseq = item.get('seq')
Found = True
break;
if not Found:
#cleanup gene name
if '*' not in gene:
gene += "*01"
gene = re.sub('-.+\*','*',gene)
for item in trfiledata:
if item.get('allele_name') == gene:
trseq = item.get('seq')
Found = True
break;
if not Found:
gene = re.sub('\*.+','',gene)
for item in trfiledata:
if item.get('gene_name') == gene:
trseq = item.get('seq')
Found = True
break;
if not Found:
#cleanup gene name(TRAV14-1*01 to TRAV14)
gene = re.sub('-.+','',gene)
for item in trfiledata:
if item.get('subgroup_name') == gene:
trseq = item.get('seq')
Found = True
break;
return trseq
def find_geneseq_from_cdr3seq(cdr3seq, trfile):
trseq = ''
if trfile:
with open(trfile, 'r') as f:
trfiledata = json.loads(f.read());
for i in range(0, len(cdr3seq)):
inseq = cdr3seq[i:]
Found = False
for item in trfiledata:
if inseq in item.get('halfseq'):
trseq = item.get('seq')
Found = True
break;
if Found:
break
return trseq
@app.route('/external_submit/<path:genelist>')
def external_submit(genelist):
glist = genelist.split(",")
trav = glist[0]
cdr3a = glist[1]
traj = glist[2]
trbv = glist[3]
cdr3b = glist[4]
trbj = glist[5]
travfile = app.root_path + '/static/genemapdata/new_TRAV_HUMAN.json';
travseq = get_seq_from_genename(trav, travfile)
trajfile = app.root_path + '/static/genemapdata/new_TRAJ_HUMAN.json';
if traj:
trajseq = get_seq_from_genename(traj, trajfile)
if not traj or trajseq == '':
trajseq = find_geneseq_from_cdr3seq(cdr3a, trajfile)
trbvfile = app.root_path + '/static/genemapdata/new_TRBV_HUMAN.json';
trbvseq = get_seq_from_genename(trbv, trbvfile)
trbjfile = app.root_path + '/static/genemapdata/new_TRBJ_HUMAN.json';
if trbj:
trbjseq = get_seq_from_genename(trbj, trbjfile)
if not trbj or trbjseq == '':
trbjseq = find_geneseq_from_cdr3seq(cdr3b, trbjfile)
aseq = travseq+cdr3a+trajseq
bseq = trbvseq+cdr3b+trbjseq
return render_template("external_submit.html",aseq=aseq,bseq=bseq)
@app.route('/external_submit1/<trav>/<traj>/<cdr3a>/<trbv>/<trbj>/<cdr3b>')
def external_submit1(trav,traj,cdr3a,trbv,trbj,cdr3b):
return render_template("external_submit.html",trav=trav,traj=traj,cdr3a=cdr3a,trbv=trbv,trbj=trbj,cdr3b=cdr3b)
'''
@app.route('/test')
def test():
return render_template("test.html")
'''
@app.route('/')
@app.route('/index')
def index():
return render_template("index.html")
@app.route('/about')
def about():
return render_template("about.html")
@app.route('/help')
def help():
return render_template("help.html")
@app.route('/links')
def links():
return render_template("links.html")
@app.route('/processjob/<aseq>/<bseq>/<loopref_checked>/<pdb_blacklist>')
def processjob(aseq,bseq,loopref_checked,pdb_blacklist):
aseq=''.join(i for i in aseq if i.isalpha())
bseq=''.join(i for i in bseq if i.isalpha())
tcrdata['aseq_user']=aseq
tcrdata['bseq_user']=bseq
a_regexp_res = get_vdomain_using_regex(aseq,"A")
if (not a_regexp_res):
errormsg = "No TCR Variable domain sequence identified from the Alpha chain input! If you used 'Select from gene', the CDR3 sequence was invalid."
return render_template("error.html", errormsg=errormsg)
a_vd_seq = a_regexp_res.groups()[0]
a_gm_seq = a_regexp_res.groups()[1]+a_regexp_res.groups()[2]
b_regexp_res = get_vdomain_using_regex(bseq,"B")
if (not b_regexp_res):
errormsg = "No TCR Variable domain sequence identified from the Beta chain input! If you used 'Select from gene', the CDR3 sequence was invalid."
return render_template("error.html", errormsg=errormsg)
b_vd_seq = b_regexp_res.groups()[0]
b_gm_seq = b_regexp_res.groups()[1]+b_regexp_res.groups()[2]
uniquedirname = create_and_cd_to_unique_dir("TCRS")#TCRS for single process
tcrdata['jobid'] = uniquedirname
#rtcrcommand = "-mute all -ignore_zero_occupancy false -renumber_pdb -per_chain_renumbering -alpha %s -beta %s -template_similarity_cutoff %s " % (aseq,bseq,simil_cutoff)
rtcrcommand = "-mute all -ignore_zero_occupancy false -renumber_pdb -per_chain_renumbering -alpha %s -beta %s -minimize_model " % (aseq,bseq)
if pdb_blacklist:
pdb_blacklist = pdb_blacklist.split(',')
with open("ignore_list.txt", 'w') as ignore_list_file:
for ignorepdb in pdb_blacklist:
ignore_list_file.write(ignorepdb+'\n')
rtcrcommand += "-ignore_list ignore_list.txt "
tcrdata['loop_ref'] = loopref_checked
looprem_checked = "no";
if (looprem_checked == "yes"):
rtcrcommand += "-remodel_tcr_cdr3_loops "
if (loopref_checked == "yes"):
rtcrcommand += "-refine_tcr_cdr3_loops -loops::max_inner_cycles 50 "
send_job_to_local_server(uniquedirname,rtcrcommand)
"""
if ( (loopref_checked == "yes") or (looprem_checked == "yes") ):
send_job_to_ibbr_cluster(uniquedirname,rtcrcommand)
#send_job_to_local_server(uniquedirname,rtcrcommand)
else:
#send_job_to_ibbr_cluster(uniquedirname,rtcrcommand)
send_job_to_local_server(uniquedirname,rtcrcommand)
"""
#find template for rendering in html
#create tcr json file with template and sequence details
a_segs = get_cdr_from_seq_by_aho_num(a_vd_seq, "A", True)
aseq_fw = a_segs[5]
aseq_cdr1 = a_segs[0]
aseq_cdr2hv4 = a_segs[2]
aseq_cdr3 = a_segs[4]
aseq_cdr3_extnd = a_segs[6]
tcrdata['aseq_vdomain'] = a_vd_seq
tcrdata['aseq_fw'] = aseq_fw
tcrdata['aseq_cdr1'] = aseq_cdr1
tcrdata['aseq_cdr2hv4'] = aseq_cdr2hv4
tcrdata['aseq_cdr3'] = aseq_cdr3
tcrdata['aseq_cdr3_extnd'] = aseq_cdr3_extnd
tcrdata['a_fw1'] = a_segs[7]
tcrdata['a_fw2'] = a_segs[8]
tcrdata['a_fw3'] = a_segs[9]
tcrdata['a_fw4'] = a_segs[10]
b_segs = get_cdr_from_seq_by_aho_num(b_vd_seq, "B", True)
bseq_fw = b_segs[5]
bseq_cdr1 = b_segs[0]
bseq_cdr2hv4 = b_segs[2]
bseq_cdr3 = b_segs[4]
bseq_cdr3_extnd = b_segs[6]
tcrdata['bseq_vdomain'] = b_vd_seq
tcrdata['bseq_fw'] = bseq_fw
tcrdata['bseq_cdr1'] = bseq_cdr1
tcrdata['bseq_cdr2hv4'] = bseq_cdr2hv4
tcrdata['bseq_cdr3'] = bseq_cdr3
tcrdata['bseq_cdr3_extnd'] = bseq_cdr3_extnd
tcrdata['b_fw1'] = b_segs[7]
tcrdata['b_fw2'] = b_segs[8]
tcrdata['b_fw3'] = b_segs[9]
tcrdata['b_fw4'] = b_segs[10]
orientation_template_file = tmplt_db_seq+"TCR_FW_ORIENTATION.seq"
ori_tmplt = find_orientation_template(aseq_fw.strip(), bseq_fw.strip(), orientation_template_file, None, pdb_blacklist)
if all(ori_tmplt):
tcrdata['ori_tmplt'] = str(ori_tmplt[0])[:4].upper()
tcrdata['ori_tmplt_Apdb'] = str(ori_tmplt[0])[:6]
tcrdata['ori_tmplt_Bpdb'] = str(ori_tmplt[1])[:6]
else:
errormsg = "No Template found for orientaion of Alpha and Beta chain sequences"
return render_template("error.html", errormsg=errormsg)
gm_multidb = glob.glob(tmplt_db_seq+"*_TCR_GM.fasta")
vd_multidb = glob.glob(tmplt_db_seq+"*_TCR_VD.fasta")
cdr1_multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR1_*.fasta")
cdr2hv4_multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR2HV4_*.fasta")
agm_tmplt = seq_match_from_fasta_files_list( a_gm_seq, gm_multidb, pdb_blacklist )
if agm_tmplt is not None:
tcrdata['acdr1_tmplt_pdb'] = str(agm_tmplt.id)[:6].upper()
tcrdata['acdr1_tmplt_pdbid'] = str(agm_tmplt.id)[:4].upper()
tcrdata['acdr1_tmplt_pdb_chain'] = str(agm_tmplt.id)[5:6].upper()
tcrdata['acdr2hv4_tmplt_pdb'] = str(agm_tmplt.id)[:6].upper()
tcrdata['acdr2hv4_tmplt_pdbid'] = str(agm_tmplt.id)[:4].upper()
tcrdata['acdr2hv4_tmplt_pdb_chain'] = str(agm_tmplt.id)[5:6].upper()
#agm_tmplt_vd_seq = seq_by_id_from_fasta_files_list(str(agm_tmplt.id), vd_multidb)
#agm_tmplt_segs = get_cdr_from_seq_by_aho_num(agm_tmplt_vd_seq, "A", True)
#tcrdata['acdr1_tmplt_seq'] = str(agm_tmplt_segs[0])
#tcrdata['acdr2hv4_tmplt_seq'] = str(agm_tmplt_segs[2])
agm_acdr1_tmplt_seq = seq_by_id_from_fasta_files_list(str(agm_tmplt.id), cdr1_multidb)
tcrdata['acdr1_tmplt_seq'] = str(agm_acdr1_tmplt_seq)
agm_acdr2hv4_tmplt_seq = seq_by_id_from_fasta_files_list(str(agm_tmplt.id), cdr2hv4_multidb)
tcrdata['acdr2hv4_tmplt_seq'] = str(agm_acdr2hv4_tmplt_seq)
else:
multidb = glob.glob(tmplt_db_seq+"*_TCR_FW.fasta")
find_templates(aseq_fw, multidb, "afw", "Alpha Framework", None, pdb_blacklist)
multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR1_*.fasta")
find_templates(aseq_cdr1, multidb, "acdr1", "Alpha CDR1", None, pdb_blacklist)
multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR2HV4_*.fasta")
find_templates(aseq_cdr2hv4, multidb, "acdr2hv4", "Alpha CDR2 & HV4", None, pdb_blacklist)
bgm_tmplt = seq_match_from_fasta_files_list( b_gm_seq, gm_multidb, pdb_blacklist )
if bgm_tmplt is not None:
tcrdata['bcdr1_tmplt_pdb'] = str(bgm_tmplt.id)[:6].upper()
tcrdata['bcdr1_tmplt_pdbid'] = str(bgm_tmplt.id)[:4].upper()
tcrdata['bcdr1_tmplt_pdb_chain'] = str(bgm_tmplt.id)[5:6].upper()
tcrdata['bcdr2hv4_tmplt_pdb'] = str(bgm_tmplt.id)[:6].upper()
tcrdata['bcdr2hv4_tmplt_pdbid'] = str(bgm_tmplt.id)[:4].upper()
tcrdata['bcdr2hv4_tmplt_pdb_chain'] = str(bgm_tmplt.id)[5:6].upper()
#bgm_tmplt_vd_seq = seq_by_id_from_fasta_files_list(str(bgm_tmplt.id), vd_multidb)
#bgm_tmplt_segs = get_cdr_from_seq_by_aho_num(bgm_tmplt_vd_seq, "B", True)
#tcrdata['bcdr1_tmplt_seq'] = str(bgm_tmplt_segs[0])
#tcrdata['bcdr2hv4_tmplt_seq'] = str(bgm_tmplt_segs[2])
bgm_acdr1_tmplt_seq = seq_by_id_from_fasta_files_list(str(bgm_tmplt.id), cdr1_multidb)
tcrdata['bcdr1_tmplt_seq'] = str(bgm_acdr1_tmplt_seq)
bgm_acdr2hv4_tmplt_seq = seq_by_id_from_fasta_files_list(str(bgm_tmplt.id), cdr2hv4_multidb)
tcrdata['bcdr2hv4_tmplt_seq'] = str(bgm_acdr2hv4_tmplt_seq)
else:
multidb = glob.glob(tmplt_db_seq+"*_TCR_FW.fasta")
find_templates(bseq_fw, multidb, "bfw", "Beta Framework", None, pdb_blacklist)
multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR1_*.fasta")
find_templates(bseq_cdr1, multidb, "bcdr1", "Beta CDR1", None, pdb_blacklist)
multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR2HV4_*.fasta")
find_templates(bseq_cdr2hv4, multidb, "bcdr2hv4", "Beta CDR2 & HV4", None, pdb_blacklist)
#CDR3
cdr3_multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR3_*.fasta")
find_templates(aseq_cdr3, cdr3_multidb, "acdr3", "Alpha CDR3", None, pdb_blacklist)
find_templates(bseq_cdr3, cdr3_multidb, "bcdr3", "Beta CDR3", None, pdb_blacklist)
#override cdr3 seq with cdr3_extnd seq
#cdr3a_tmplt_vd_seq = seq_by_id_from_fasta_files_list(tcrdata['acdr3_tmplt_id'], vd_multidb)
#print "cdr3a_tmplt_vd_seq", cdr3a_tmplt_vd_seq
#cdr3a_tmplt_segs = get_cdr_from_seq_by_aho_num(cdr3a_tmplt_vd_seq, None, True)
#tcrdata['acdr3_tmplt_seq'] = str(cdr3a_tmplt_segs[6])
#cdr3b_tmplt_vd_seq = seq_by_id_from_fasta_files_list(tcrdata['bcdr3_tmplt_id'], vd_multidb)
#cdr3b_tmplt_segs = get_cdr_from_seq_by_aho_num(cdr3b_tmplt_vd_seq, None, True)
#tcrdata['bcdr3_tmplt_seq'] = str(cdr3b_tmplt_segs[6])
cdr3extnd_multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR3extnd_*.fasta")
acdr3extnd_tmplt_seq = seq_by_id_from_fasta_files_list(tcrdata['acdr3_tmplt_id'], cdr3extnd_multidb)
tcrdata['acdr3_tmplt_seq'] = str(acdr3extnd_tmplt_seq)
bcdr3extnd_tmplt_seq = seq_by_id_from_fasta_files_list(tcrdata['bcdr3_tmplt_id'], cdr3extnd_multidb)
tcrdata['bcdr3_tmplt_seq'] = str(bcdr3extnd_tmplt_seq)
with open(uniquedirname+'.json', 'w') as tcr_json_file:
js = json.dumps(tcrdata)
tcr_json_file.write(js+"\n")
return redirect(url_for('rtcr', jobid=uniquedirname))
@app.route('/process_tcrpmhc_job/<aseq>/<bseq>/<pseq>/<mhc1aseq>/<mhc2aseq>/<mhc2bseq>/<loopref_checked>/<pdb_blacklist>')
def process_tcrpmhc_job(aseq,bseq,pseq,mhc1aseq,mhc2aseq,mhc2bseq,loopref_checked,pdb_blacklist):
aseq=''.join(i for i in aseq if i.isalpha())
bseq=''.join(i for i in bseq if i.isalpha())
tcrdata['aseq_user']=aseq
tcrdata['bseq_user']=bseq
a_regexp_res = get_vdomain_using_regex(aseq,"A")
if (not a_regexp_res):
errormsg = "No TCR Variable domain sequence identified from the Alpha chain input! If you used 'Select from gene', the CDR3 sequence was invalid."
return render_template("error.html", errormsg=errormsg)
a_vd_seq = a_regexp_res.groups()[0]
a_gm_seq = a_regexp_res.groups()[1]+a_regexp_res.groups()[2]
b_regexp_res = get_vdomain_using_regex(bseq,"B")
if (not b_regexp_res):
errormsg = "No TCR variable domain sequence identified from the Beta chain input! If you used 'Select from gene', the CDR3 sequence was invalid."
return render_template("error.html", errormsg=errormsg)
b_vd_seq = b_regexp_res.groups()[0]
b_gm_seq = b_regexp_res.groups()[1]+b_regexp_res.groups()[2]
#we use uniquedirname to differentiate mhc1 and mhc2 complexes in res_tcrpmhc function
if (not mhc1aseq == 'NA'):
uniquedirname = create_and_cd_to_unique_dir("MHC1")#TCRC for tcr-p-mhc complex
pseq=''.join(i for i in pseq if i.isalpha())
mhc1aseq=''.join(i for i in mhc1aseq if i.isalpha())
tcrdata['pep'] = pseq
tcrdata['mhc1a'] = mhc1aseq
rtcrcommand = "-blastp_path /www/cgi-bin/ncbi-blast-2.12.0+/bin/blastp -mute all -ignore_zero_occupancy false -renumber_pdb -per_chain_renumbering -alpha %s -beta %s -peptide %s -mhc1_alpha %s " % (aseq, bseq, pseq, mhc1aseq)
elif ( (not mhc2aseq == 'NA') and (not mhc2bseq == 'NA') ):
uniquedirname = create_and_cd_to_unique_dir("MHC2")#TCRC for tcr-p-mhc complex
core_pseq = get_core_binding_pepseq(pseq)
mhc2aseq=''.join(i for i in mhc2aseq if i.isalpha())
mhc2bseq=''.join(i for i in mhc2bseq if i.isalpha())
tcrdata['trunc_pep'] = core_pseq
tcrdata['mhc2a'] = mhc2aseq
tcrdata['mhc2b'] = mhc2bseq
rtcrcommand = "-blastp_path /www/cgi-bin/ncbi-blast-2.12.0+/bin/blastp -mute all -ignore_zero_occupancy false -renumber_pdb -per_chain_renumbering -alpha %s -beta %s -peptide %s -mhc2_alpha %s -mhc2_beta %s " % (aseq, bseq, core_pseq, mhc2aseq, mhc2bseq)
tcrdata['jobid'] = uniquedirname
if pdb_blacklist:
pdb_blacklist = pdb_blacklist.split(',')
with open("ignore_list.txt", 'w') as ignore_list_file:
for ignorepdb in pdb_blacklist:
ignore_list_file.write(ignorepdb+'\n')
rtcrcommand += "-ignore_list ignore_list.txt "
#use -include_list include_list.txt flag to model on specific template
#create a file with specific template name
#rtcrcommand += "-include_list include_list.txt "
tcrdata['loop_ref'] = loopref_checked
looprem_checked = "no";
if (looprem_checked == "yes"):
rtcrcommand += "-remodel_tcr_cdr3_loops "
if (loopref_checked == "yes"):
rtcrcommand += "-refine_tcr_cdr3_loops -loops::max_inner_cycles 50 "
send_tcrpmhc_job_to_local_server(uniquedirname,rtcrcommand)
"""
if ( (loopref_checked == "yes") or (looprem_checked == "yes") ):
#send_job_to_ibbr_cluster(uniquedirname,rtcrcommand)
send_tcrpmhc_job_to_local_server(uniquedirname,rtcrcommand)
else:
#send_job_to_ibbr_cluster(uniquedirname,rtcrcommand)
send_tcrpmhc_job_to_local_server(uniquedirname,rtcrcommand)
"""
#find template for rendering in html
#create tcr json file with template and sequence details
a_segs = get_cdr_from_seq_by_aho_num(a_vd_seq, "A", True)
aseq_fw = a_segs[5]
aseq_cdr1 = a_segs[0]
aseq_cdr2hv4 = a_segs[2]
aseq_cdr3 = a_segs[4]
aseq_cdr3_extnd = a_segs[6]
tcrdata['aseq_vdomain'] = a_vd_seq
tcrdata['aseq_fw'] = aseq_fw
tcrdata['aseq_cdr1'] = aseq_cdr1
tcrdata['aseq_cdr2hv4'] = aseq_cdr2hv4
tcrdata['aseq_cdr3'] = aseq_cdr3
tcrdata['aseq_cdr3_extnd'] = aseq_cdr3_extnd
tcrdata['a_fw1'] = a_segs[7]
tcrdata['a_fw2'] = a_segs[8]
tcrdata['a_fw3'] = a_segs[9]
tcrdata['a_fw4'] = a_segs[10]
b_segs = get_cdr_from_seq_by_aho_num(b_vd_seq, "B", True)
bseq_fw = b_segs[5]
bseq_cdr1 = b_segs[0]
bseq_cdr2hv4 = b_segs[2]
bseq_cdr3 = b_segs[4]
bseq_cdr3_extnd = b_segs[6]
tcrdata['bseq_vdomain'] = b_vd_seq
tcrdata['bseq_fw'] = bseq_fw
tcrdata['bseq_cdr1'] = bseq_cdr1
tcrdata['bseq_cdr2hv4'] = bseq_cdr2hv4
tcrdata['bseq_cdr3'] = bseq_cdr3
tcrdata['bseq_cdr3_extnd'] = bseq_cdr3_extnd
tcrdata['b_fw1'] = b_segs[7]
tcrdata['b_fw2'] = b_segs[8]
tcrdata['b_fw3'] = b_segs[9]
tcrdata['b_fw4'] = b_segs[10]
orientation_template_file = tmplt_db_seq+"TCR_FW_ORIENTATION.seq"
ori_tmplt = find_orientation_template(aseq_fw.strip(), bseq_fw.strip(), orientation_template_file, None, pdb_blacklist)
if all(ori_tmplt):
tcrdata['ori_tmplt'] = str(ori_tmplt[0])[:4].upper()
tcrdata['ori_tmplt_Apdb'] = str(ori_tmplt[0])[:6]
tcrdata['ori_tmplt_Bpdb'] = str(ori_tmplt[1])[:6]
else:
errormsg = "No Template found for orientaion of Alpha and Beta chain sequences"
return render_template("error.html", errormsg=errormsg)
gm_multidb = glob.glob(tmplt_db_seq+"*_TCR_GM.fasta")
vd_multidb = glob.glob(tmplt_db_seq+"*_TCR_VD.fasta")
cdr1_multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR1_*.fasta")
cdr2hv4_multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR2HV4_*.fasta")
agm_tmplt = seq_match_from_fasta_files_list( a_gm_seq, gm_multidb, pdb_blacklist )
if agm_tmplt is not None:
tcrdata['acdr1_tmplt_pdb'] = str(agm_tmplt.id)[:6].upper()
tcrdata['acdr1_tmplt_pdbid'] = str(agm_tmplt.id)[:4].upper()
tcrdata['acdr1_tmplt_pdb_chain'] = str(agm_tmplt.id)[5:6].upper()
tcrdata['acdr2hv4_tmplt_pdb'] = str(agm_tmplt.id)[:6].upper()
tcrdata['acdr2hv4_tmplt_pdbid'] = str(agm_tmplt.id)[:4].upper()
tcrdata['acdr2hv4_tmplt_pdb_chain'] = str(agm_tmplt.id)[5:6].upper()
#agm_tmplt_vd_seq = seq_by_id_from_fasta_files_list(str(agm_tmplt.id), vd_multidb)
#agm_tmplt_segs = get_cdr_from_seq_by_aho_num(agm_tmplt_vd_seq, "A", True)
#tcrdata['acdr1_tmplt_seq'] = str(agm_tmplt_segs[0])
#tcrdata['acdr2hv4_tmplt_seq'] = str(agm_tmplt_segs[2])
agm_acdr1_tmplt_seq = seq_by_id_from_fasta_files_list(str(agm_tmplt.id), cdr1_multidb)
tcrdata['acdr1_tmplt_seq'] = str(agm_acdr1_tmplt_seq)
agm_acdr2hv4_tmplt_seq = seq_by_id_from_fasta_files_list(str(agm_tmplt.id), cdr2hv4_multidb)
tcrdata['acdr2hv4_tmplt_seq'] = str(agm_acdr2hv4_tmplt_seq)
else:
multidb = glob.glob(tmplt_db_seq+"*_TCR_FW.fasta")
find_templates(aseq_fw, multidb, "afw", "Alpha Framework", None, pdb_blacklist)
multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR1_*.fasta")
find_templates(aseq_cdr1, multidb, "acdr1", "Alpha CDR1", None, pdb_blacklist)
multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR2HV4_*.fasta")
find_templates(aseq_cdr2hv4, multidb, "acdr2hv4", "Alpha CDR2 & HV4", None, pdb_blacklist)
bgm_tmplt = seq_match_from_fasta_files_list( b_gm_seq, gm_multidb, pdb_blacklist )
if bgm_tmplt is not None:
tcrdata['bcdr1_tmplt_pdb'] = str(bgm_tmplt.id)[:6].upper()
tcrdata['bcdr1_tmplt_pdbid'] = str(bgm_tmplt.id)[:4].upper()
tcrdata['bcdr1_tmplt_pdb_chain'] = str(bgm_tmplt.id)[5:6].upper()
tcrdata['bcdr2hv4_tmplt_pdb'] = str(bgm_tmplt.id)[:6].upper()
tcrdata['bcdr2hv4_tmplt_pdbid'] = str(bgm_tmplt.id)[:4].upper()
tcrdata['bcdr2hv4_tmplt_pdb_chain'] = str(bgm_tmplt.id)[5:6].upper()
#bgm_tmplt_vd_seq = seq_by_id_from_fasta_files_list(str(bgm_tmplt.id), vd_multidb)
#bgm_tmplt_segs = get_cdr_from_seq_by_aho_num(bgm_tmplt_vd_seq, "B", True)
#tcrdata['bcdr1_tmplt_seq'] = str(bgm_tmplt_segs[0])
#tcrdata['bcdr2hv4_tmplt_seq'] = str(bgm_tmplt_segs[2])
bgm_acdr1_tmplt_seq = seq_by_id_from_fasta_files_list(str(bgm_tmplt.id), cdr1_multidb)
tcrdata['bcdr1_tmplt_seq'] = str(bgm_acdr1_tmplt_seq)
bgm_acdr2hv4_tmplt_seq = seq_by_id_from_fasta_files_list(str(bgm_tmplt.id), cdr2hv4_multidb)
tcrdata['bcdr2hv4_tmplt_seq'] = str(bgm_acdr2hv4_tmplt_seq)
else:
multidb = glob.glob(tmplt_db_seq+"*_TCR_FW.fasta")
find_templates(bseq_fw, multidb, "bfw", "Beta Framework", None, pdb_blacklist)
multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR1_*.fasta")
find_templates(bseq_cdr1, multidb, "bcdr1", "Beta CDR1", None, pdb_blacklist)
multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR2HV4_*.fasta")
find_templates(bseq_cdr2hv4, multidb, "bcdr2hv4", "Beta CDR2 & HV4", None, pdb_blacklist)
#CDR3
cdr3_multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR3_*.fasta")
find_templates(aseq_cdr3, cdr3_multidb, "acdr3", "Alpha CDR3", None, pdb_blacklist)
find_templates(bseq_cdr3, cdr3_multidb, "bcdr3", "Beta CDR3", None, pdb_blacklist)
#override cdr3 seq with cdr3_extnd seq
#cdr3a_tmplt_vd_seq = seq_by_id_from_fasta_files_list(tcrdata['acdr3_tmplt_id'], vd_multidb)
#print "cdr3a_tmplt_vd_seq", cdr3a_tmplt_vd_seq
#cdr3a_tmplt_segs = get_cdr_from_seq_by_aho_num(cdr3a_tmplt_vd_seq, None, True)
#tcrdata['acdr3_tmplt_seq'] = str(cdr3a_tmplt_segs[6])
#cdr3b_tmplt_vd_seq = seq_by_id_from_fasta_files_list(tcrdata['bcdr3_tmplt_id'], vd_multidb)
#cdr3b_tmplt_segs = get_cdr_from_seq_by_aho_num(cdr3b_tmplt_vd_seq, None, True)
#tcrdata['bcdr3_tmplt_seq'] = str(cdr3b_tmplt_segs[6])
cdr3extnd_multidb = glob.glob(tmplt_db_seq+"*_TCR_CDR3extnd_*.fasta")
acdr3extnd_tmplt_seq = seq_by_id_from_fasta_files_list(tcrdata['acdr3_tmplt_id'], cdr3extnd_multidb)
tcrdata['acdr3_tmplt_seq'] = str(acdr3extnd_tmplt_seq)
bcdr3extnd_tmplt_seq = seq_by_id_from_fasta_files_list(tcrdata['bcdr3_tmplt_id'], cdr3extnd_multidb)
tcrdata['bcdr3_tmplt_seq'] = str(bcdr3extnd_tmplt_seq)
with open(uniquedirname+'.json', 'w') as tcr_json_file:
js = json.dumps(tcrdata)
tcr_json_file.write(js+"\n")
return redirect(url_for('res_tcrpmhc', jobid=uniquedirname))
def send_job_to_local_server(uniquedirname,rtcrcommand):
#rtcrcommand += " -tcr_template_db_path /www/tcrmodel/static/downloads/additional_protocol_data/tcr/"
rtcrcommand += " -tcr_template_db_path /www/cgi-bin/rosetta/Rosetta/main/database/additional_protocol_data/tcr/"
commandline = "/www/cgi-bin/rosetta/Rosetta/main/source/bin/tcrmodel.static.linuxgccrelease -database /www/cgi-bin/rosetta/Rosetta/main/database " + rtcrcommand + " > res.out "
p = subprocess.Popen(commandline, shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
#out,err = p.communicate()
#Do not call communicate if you do not want to wait for the command to complete
return
def send_tcrpmhc_job_to_local_server(uniquedirname,rtcrcommand):
#rtcrcommand += " -tcr_template_db_path /www/tcrmodel/static/downloads/additional_protocol_data/tcr/"
rtcrcommand += " -tcr_template_db_path /www/cgi-bin/rosetta/Rosetta/main/database/additional_protocol_data/tcr/"
commandline = "/www/cgi-bin/rosetta/Rosetta/main/source/bin/tcr_complex_model.static.linuxgccrelease -database /www/cgi-bin/rosetta/Rosetta/main/database " + rtcrcommand + " > res.out "
commandline2 = "echo " + commandline + " > ros_cmd.txt"
p = subprocess.Popen(commandline, shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p2 = subprocess.Popen(commandline2, shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
#out,err = p.communicate()
#Do not call communicate if you do not want to wait for the command to complete
#print stdout
#print stderr
return
def send_job_to_ibbr_cluster(uniquejobid,rtcrcommand):
jobscriptfile = "RosettaTCR.slurm"
pbs_file_path = os.path.join(rundir_path,uniquejobid,jobscriptfile)
ig_fn = "ignore_list.txt"
with open(pbs_file_path, 'a') as f:
f.write('#!/bin/sh\n')
f.write('#SBATCH -n 16\n')
f.write('#SBATCH --time 72:00:00\n')
f.write('#SBATCH --mem=512M\n')
f.write('cd $SLURM_SUBMIT_DIR\n')
f.write('rundir=${PWD##*/}\n')
commandline = "/home/gowthamanr/Rosetta/main/source/bin/tcrmodel.static.linuxgccrelease " + rtcrcommand + " > res.out "
f.write(commandline+'\n')
f.write("if test -f res.out ; then scp res.out [email protected]:"+rundir_path+"/$rundir/res.out ;fi\n")
f.write("chmod 777 $SLURM_SUBMIT_DIR/tcrmodel.pdb\n")
f.write("if test -f tcrmodel.pdb ; then scp tcrmodel.pdb [email protected]:"+rundir_path+"/$rundir/tcrmodel.pdb ;fi\n")
f.write("if ! test -f tcrmodel.pdb ; then echo ERROR > tcr.fail; scp tcr.fail [email protected]:"+rundir_path+"/$rundir/tcr.fail ;fi\n")
submit_job_on_cluster(uniquejobid,jobscriptfile,ig_fn)
return
def renumber_tcrpdb_by_aho_number(outpdb):
outpdb_orig = 'tcrmodel.pdb.orig'
tcr_achain = 'tcr_achain.pdb'
tcr_bchain = 'tcr_bchain.pdb'
tcr_achain_aho = 'tcr_achain_aho.pdb'
tcr_bchain_aho = 'tcr_bchain_aho.pdb'
make_pdb(outpdb, "A", tcr_achain)
make_pdb(outpdb, "B", tcr_bchain)
renumber_pdbfile_to_aho(tcr_achain, "A", tcr_achain_aho, True)
renumber_pdbfile_to_aho(tcr_bchain, "B", tcr_bchain_aho, True)
if ( (os.path.isfile(tcr_achain_aho) and os.path.getsize(tcr_achain_aho) > 0)
and (os.path.isfile(tcr_bchain_aho) and os.path.getsize(tcr_bchain_aho) > 0) ):
shutil.move(outpdb, outpdb_orig)
with open(outpdb,'wb') as wfd:
for f in [tcr_achain_aho, tcr_bchain_aho]:
with open(f,'rb') as fd:
shutil.copyfileobj(fd, wfd, 1024*1024*10)
return
def add_ss_header_to_pdbfile(outpdb):
dsspfile = "tcrmodel.dssp"
ssheaderfile = "tcrmodel_ssheader.pdb"
tcr_ss_tmp_pdb = "tcrmodel.tmp.pdb"
dssp2pdb_script = os.path.join(app.root_path, "dssp2pdb.pl")
subprocess.call(["/www/cgi-bin/dssp-3.0.0/mkdssp", outpdb, dsspfile])
if ( os.path.isfile(dsspfile) and (os.path.getsize(dsspfile)>0) ):
with open(ssheaderfile, 'w') as outfile:
subprocess.call(["perl", dssp2pdb_script, "-35", dsspfile], stdout=outfile)
if ( os.path.isfile(ssheaderfile) and (os.path.getsize(ssheaderfile)>0) ):
with open(tcr_ss_tmp_pdb,'w') as wfd:
for f in [ssheaderfile, outpdb]:
with open(f,'rb') as fd:
shutil.copyfileobj(fd, wfd)
shutil.move(tcr_ss_tmp_pdb, outpdb)
return
def create_profit_infile_cdr1(infile,refchain,mobchain,outpdb):
f = open(infile,"w")
f.write("ATOMS N,CA,C\n")
f.write("ZONE CLEAR\n")
f.write("ZONE "+refchain+"23"+"-"+refchain+"44"+":"+mobchain+"23"+"-"+mobchain+"44"+"\n")
f.write("FIT\n")
f.write("WRITE "+outpdb+"\n")
f.close()
def create_profit_infile_cdr3(infile,refchain,mobchain,outpdb):
f = open(infile,"w")
f.write("ATOMS N,CA,C\n")
f.write("ZONE CLEAR\n")
f.write("ZONE "+refchain+"107"+"-"+refchain+"138"+":"+mobchain+"107"+"-"+mobchain+"138"+"\n")
f.write("FIT\n")
f.write("WRITE "+outpdb+"\n")
f.close()
def create_profit_infile_cdr2hv4(infile,refchain,mobchain,outpdb):
f = open(infile,"w")
f.write("ATOMS N,CA,C\n")
f.write("ZONE CLEAR\n")
f.write("ZONE "+refchain+"56"+"-"+refchain+"70"+":"+mobchain+"56"+"-"+mobchain+"70"+"\n")
f.write("FIT\n")
f.write("WRITE "+outpdb+"\n")
f.close()
def create_profit_infile_ori(infile,refchain,mobchain,outpdb):
f = open(infile,"w")
f.write("ATOMS N,CA,C\n")
f.write("ZONE CLEAR\n")
f.write("ZONE "+refchain+"4"+"-"+refchain+"23"+":"+mobchain+"4"+"-"+mobchain+"23"+"\n")
f.write("ZONE "+refchain+"44"+"-"+refchain+"56"+":"+mobchain+"44"+"-"+mobchain+"56"+"\n")
f.write("ZONE "+refchain+"70"+"-"+refchain+"107"+":"+mobchain+"70"+"-"+mobchain+"107"+"\n")
f.write("ZONE "+refchain+"138"+"-"+refchain+"148"+":"+mobchain+"138"+"-"+mobchain+"148"+"\n")
f.write("FIT\n")
f.write("WRITE "+outpdb+"\n")
f.close()
def align_tmplt_and_target(infile, reference, mobile):
profit_program = "profit"
cmd = subprocess.Popen([profit_program, '-f', infile, '-h', reference, mobile], stdout=subprocess.PIPE)
return
def get_pdb_templates(tcrjsondata):
ref = "tcrmodel.pdb"
refchainA = "A"
refchainB = "B"
#cdr1a
mob = glob.glob(tmplt_db_pdb+tcrjsondata['acdr1_tmplt_pdb'][:4].lower()+"_aho.pdb.gz")[0]
mobchain = tcrjsondata['acdr1_tmplt_pdb'][5:6]
acdr1_outpdb = tcrjsondata['acdr1_tmplt_pdb'] + "_Acdr1_tmplt.pdb"
infile = "Acdr1_profit.in"
create_profit_infile_cdr1(infile,refchainA,mobchain,acdr1_outpdb)
align_tmplt_and_target(infile,ref,mob)
#cdr2a
mob = glob.glob(tmplt_db_pdb+tcrjsondata['acdr2hv4_tmplt_pdb'][:4].lower()+"_aho.pdb.gz")[0]
mobchain = tcrjsondata['acdr2hv4_tmplt_pdb'][5:6]
acdr2hv4_outpdb = tcrjsondata['acdr2hv4_tmplt_pdb'] + "_Acdr2hv4_tmplt.pdb"
infile = "Acdr2hv4_profit.in"
create_profit_infile_cdr2hv4(infile,refchainA,mobchain,acdr2hv4_outpdb)
align_tmplt_and_target(infile,ref,mob)
#cdr3a
mob = glob.glob(tmplt_db_pdb+tcrjsondata['acdr3_tmplt_pdb'][:4].lower()+"_aho.pdb.gz")[0]
mobchain = tcrjsondata['acdr3_tmplt_pdb'][5:6]
acdr3_outpdb = tcrjsondata['acdr3_tmplt_pdb'] + "_Acdr3_tmplt.pdb"
infile = "Acdr3_profit.in"
create_profit_infile_cdr3(infile,refchainA,mobchain,acdr3_outpdb)
align_tmplt_and_target(infile,ref,mob)
#cdr1b
mob = glob.glob(tmplt_db_pdb+tcrjsondata['bcdr1_tmplt_pdb'][:4].lower()+"_aho.pdb.gz")[0]
mobchain = tcrjsondata['bcdr1_tmplt_pdb'][5:6]
bcdr1_outpdb = tcrjsondata['bcdr1_tmplt_pdb'] + "_Bcdr1_tmplt.pdb"
infile = "Bcdr1_profit.in"
create_profit_infile_cdr1(infile,refchainB,mobchain,bcdr1_outpdb)
align_tmplt_and_target(infile,ref,mob)
#cdr2b
mob = glob.glob(tmplt_db_pdb+tcrjsondata['bcdr2hv4_tmplt_pdb'][:4].lower()+"_aho.pdb.gz")[0]
mobchain = tcrjsondata['bcdr2hv4_tmplt_pdb'][5:6]
bcdr2hv4_outpdb = tcrjsondata['bcdr2hv4_tmplt_pdb'] + "_Bcdr2hv4_tmplt.pdb"
infile = "Bcdr2hv4_profit.in"
create_profit_infile_cdr2hv4(infile,refchainB,mobchain,bcdr2hv4_outpdb)
align_tmplt_and_target(infile,ref,mob)
#cdr3b
mob = glob.glob(tmplt_db_pdb+tcrjsondata['bcdr3_tmplt_pdb'][:4].lower()+"_aho.pdb.gz")[0]
mobchain = tcrjsondata['bcdr3_tmplt_pdb'][5:6]
bcdr3_outpdb = tcrjsondata['bcdr3_tmplt_pdb'] + "_Bcdr3_tmplt.pdb"
infile = "Bcdr3_profit.in"
create_profit_infile_cdr3(infile,refchainB,mobchain,bcdr3_outpdb)
align_tmplt_and_target(infile,ref,mob)
#orientation templates
#orientation A
mob = glob.glob(tmplt_db_pdb+tcrjsondata['ori_tmplt_Apdb'][:4].lower()+"_aho.pdb.gz")[0]
mobchain = tcrjsondata['ori_tmplt_Apdb'][5:6]
oria_outpdb = tcrjsondata['ori_tmplt_Apdb'] + "_oriA_tmplt.pdb"
infile = "oriA_profit.in"
create_profit_infile_ori(infile,refchainA,mobchain,oria_outpdb)
align_tmplt_and_target(infile,ref,mob)
#orientation B
mob = glob.glob(tmplt_db_pdb+tcrjsondata['ori_tmplt_Bpdb'][:4].lower()+"_aho.pdb.gz")[0]
mobchain = tcrjsondata['ori_tmplt_Bpdb'][5:6]
orib_outpdb = tcrjsondata['ori_tmplt_Bpdb'] + "_oriB_tmplt.pdb"
infile = "oriB_profit.in"
create_profit_infile_ori(infile,refchainB,mobchain,orib_outpdb)
align_tmplt_and_target(infile,ref,mob)
'''
tar_filename = tcrjsondata['jobid'] + ".tar.gz"
from contextlib import closing
with closing(tarfile.open(tar_filename, "w:gz")) as tar:
for name in [ "tcrmodel.pdb", acdr1_outpdb, acdr2hv4_outpdb, acdr3_outpdb, bcdr1_outpdb, bcdr2hv4_outpdb, bcdr3_outpdb, oria_outpdb,orib_outpdb]:
tar.add(name)
'''
return
def unzip(gz, pdb):
if not os.path.isfile(pdb):
with gzip.open(gz) as f:
contents = f.read()
with open(pdb, "w") as f:
f.write(contents)
def find_tmplt(pdb_id):
tmplt = glob.glob(tmplt_db_tcrpmhc + pdb_id + ".trunc.fit.pdb")
tmplt = tmplt[0] if tmplt else glob.glob(tmplt_db_pdb + pdb_id + "_aho.pdb.gz")[0]
if tmplt[-3:] == ".gz":
unzipped = pdb_id + "_unzipped.pdb"
unzip(tmplt, unzipped)
tmplt = unzipped
return tmplt
"""
def grab_chain(infile, chain, outfile):
if not os.path.isfile(outfile):
perl_script = "../../cgi-bin/scripts/grab_chains.pl"
subprocess.Popen([perl_script, infile, chain, ">", outfile], stdout=subprocess.PIPE)
"""
def grab_chain(infile, chain, outfile):
if not os.path.isfile(outfile):
with open(infile) as f:
lines = f.read().split("\n")
with open(outfile, "w") as f:
for l in lines:
if l[:4] == "ATOM" or l[:6] == "HETATM":
ch = l[21]
if ch == chain:
f.write(l + "\n")
def run_tmalign(tmplt, model, outfile):
if not os.path.isfile(outfile):
tmalign_program = "../../cgi-bin/TMalign/TMalign"
subprocess.Popen([tmalign_program, tmplt, model, "-o", outfile], stdout=subprocess.PIPE)
def get_tcrpmhc_templates(tcrjsondata):
model = "tcrpmhc_model.pdb"
acdr_tmplts = ["acdr1", "acdr2hv4", "acdr3"]
bcdr_tmplts = ["bcdr1", "bcdr2hv4", "bcdr3"]
model_D = model[:-4] + "_D.pdb"
model_E = model[:-4] + "_E.pdb"
grab_chain(model, "D", model_D)
grab_chain(model, "E", model_E)
#cdr tmplts
for t in acdr_tmplts:
t += "_tmplt"
tmplt_id = tcrjsondata[t+"_id"]
pdb_id = tmplt_id[:4].lower()
tmplt = find_tmplt(pdb_id)
tmplt_D = pdb_id + "_D_chain.pdb"
grab_chain(tmplt, tmplt_id[-1], tmplt_D)
outfile = tmplt_id + "_" + t[0].upper() + t[1:] + ".sup"
run_tmalign(tmplt_D, model_D, outfile)
for t in bcdr_tmplts:
t += "_tmplt"
tmplt_id = tcrjsondata[t+"_id"]
pdb_id = tmplt_id[:4].lower()
tmplt = find_tmplt(pdb_id)
tmplt_E = pdb_id + "_E_chain.pdb"
grab_chain(tmplt, tmplt_id[-1], tmplt_E)
outfile = tmplt_id + "_" + t[0].upper() + t[1:] + ".sup"
run_tmalign(tmplt_E, model_E, outfile)
#ori tmplt
tmplt_id = tcrjsondata['aori_tmplt_id']
pdb_id = tmplt_id[:4].lower()
tmplt = find_tmplt(pdb_id)
outfile = tmplt_id + "_ori_tmplt.sup"
run_tmalign(tmplt, model, outfile)
@app.route('/rtcr/<jobid>')
def rtcr(jobid):
outdir = os.path.join(rundir_path,str(jobid))
if not os.path.exists(outdir):
return render_template("error.html", errormsg="Job ID not found")
os.chdir(outdir)
tcrjsonfile = os.path.join(outdir,str(jobid)+'.json')
tcrjsonfile_spath = os.path.join(rundir_spath,str(jobid),str(jobid)+'.json')
with open(tcrjsonfile) as json_data:
tcrjsondata = json.load(json_data)
outpdb = os.path.join(outdir,'tcrmodel.pdb')
errorfile = os.path.join(outdir,'tcr.fail')
errorfile2 = os.path.join(outdir,'ROSETTA_CRASH.log')
if os.path.isfile(outpdb):
renumber_tcrpdb_by_aho_number(outpdb)
add_ss_header_to_pdbfile(outpdb)
outpdb_spath = os.path.join(rundir_spath,str(jobid),'tcrmodel.pdb')
stdout = get_pdb_templates(tcrjsondata)
return render_template("tcrmodel_completed.html", rtcrjobid = jobid, modelfname=outpdb_spath, tj=tcrjsondata)
elif os.path.isfile(errorfile):
return render_template("error.html", jobid=jobid, errormsg="Modeling could not complete!")
elif os.path.isfile(errorfile2):
errormsg = "Modeling could not complete!"
with open(errorfile2) as fh:
for line in fh:
if line.startswith("ERROR:"):
errormsg = line[7:]
break
return render_template("error.html", jobid=jobid, errormsg=errormsg)
else:
steps = ["Job started!", "Selecting templates..."]
if os.path.isfile("ignore_list.txt"):
steps.append("Running Rosetta...")
if os.path.isfile(str(jobid)+".json"):
if tcrdata['loop_ref'] == "yes":
steps.append("Grafting model + refining CDR loops...")
else:
steps.append("Grafting model...")
if os.path.isfile("tcrgraftmodel.pdb"):
steps.append("Orienting templates and refining structure...")
if tcrdata['loop_ref'] == "yes":
approx_time = "5 or 6 minutes"
else:
approx_time = "1 minute"
return render_template("rtcrqueued.html", jobid=jobid, approx_time=approx_time, steps=steps)
@app.route('/res_tcrpmhc/<jobid>')
def res_tcrpmhc(jobid):
outdir = os.path.join(rundir_path,str(jobid))
if not os.path.exists(outdir):
return render_template("error.html", errormsg="Job ID not found")
os.chdir(outdir)
modelpdb = os.path.join(outdir,'tcrpmhc_model.pdb')
errorfile = os.path.join(outdir,'tcr.fail')
errorfile2 = os.path.join(outdir,'ROSETTA_CRASH.log')
if os.path.isfile(modelpdb):
#run model delsection here?
renamed_chain_file = "renamed_chain.pdb"
renum_aho_file = "renum_aho.pdb"
ss_header_file = "tcrmodel_ssheader.pdb"
if not os.path.isfile(renamed_chain_file):
if (jobid[:4] == "MHC1"):
rename_pdb_chains("ABCD", "ACDE", modelpdb, renamed_chain_file )
if (jobid[:4] == "MHC2"):
rename_pdb_chains("ABCDE", "ABCDE", modelpdb, renamed_chain_file )
if not os.path.isfile(renum_aho_file):
renumber_pdbchain_to_aho(renamed_chain_file, "D", None, "ahoD.pdb", True)
renumber_pdbchain_to_aho("ahoD.pdb", "E", None, renum_aho_file, True)
if (os.path.isfile(renum_aho_file) and os.path.getsize(renum_aho_file) > 0):
shutil.copyfile(renum_aho_file, modelpdb)
if not os.path.isfile(ss_header_file):
add_ss_header_to_pdbfile(modelpdb)
outpdb_spath = os.path.join(rundir_spath,str(jobid),'tcrpmhc_model.pdb')
#Read Json file and change empty '' values to 'NA' values
tcrjsonfile = os.path.join(outdir,"tcr_template_info.json")
with open(tcrjsonfile) as json_data:
tcrjsondata = json.load(json_data)
for key in tcrjsondata:
if not tcrjsondata[key]:
tcrjsondata[key] = 'NA';
stdout = get_tcrpmhc_templates(tcrjsondata)
from datetime import datetime
now = datetime.now()
current_time = now.strftime("%H:%M:%S")
print("Current Time =", current_time)
return render_template("tcrpmhc_completed.html", jobid=jobid, modelfname=outpdb_spath, tj=tcrjsondata)
elif os.path.isfile(errorfile):
return render_template("error.html", jobid=jobid, errormsg="Modeling could not complete!")
elif os.path.isfile(errorfile2):
errormsg = "Modeling could not complete!"
with open(errorfile2) as fh:
for line in fh:
if line.startswith("ERROR:"):
errormsg = line[7:]
break
return render_template("error.html", jobid=jobid, errormsg=errormsg)
else:
steps = ["Job started!", "Selecting templates..."]
if os.path.isfile("ignore_list.txt"):
steps.append("Running Rosetta...")
if os.path.isfile(str(jobid)+".json"):
steps.append("Querying MHC...")
if os.path.isfile("mhc1a_blastp.out") or os.path.isfile("mhc2b_blastp.out"):
steps.append("Grafting model...")
if os.path.isfile("tcrgraftmodel.pdb"):
steps.append("Orienting templates and refining structure...")
return render_template("tcrpmhc_queued.html", jobid=jobid, steps=steps)
@app.route('/mtcr/<jobid>')
def mtcr(jobid):
outdir = os.path.join(rundir_path,str(jobid))
if not os.path.exists(outdir):
return render_template("error.html", errormsg="Job ID not found")
os.chdir(outdir)
tcrjsonfile = os.path.join(outdir,str(jobid)+'.json')
with open(tcrjsonfile) as json_data:
tcrjsondata = json.load(json_data)