percolatorPeptides = per.getPeptides(elems)
uniquePeptides = set([pept.peptide for pept in percolatorPeptides])
prosolvePeptides = list()
f = open(infile2).readlines()
#(self,isdecoy=False,pep=0.0,q=0.0,empq=0.0,p=0.0,sequence="",score=0.0,psms=[],proteins=[]):
for line in f:
words = line.split()
prob = float(words[0])
sequence = str(words[1])
proteins = list(words[2:])
isdecoy = False
if(str(proteins[0]).find(decoy_pattern) != -1 ):
isdecoy = True
peptide = hit.Peptide(isdecoy,float(1 - prob),float(0.0),float(0.0),float(0.0),str(sequence),float(prob),[],proteins)
if(sequence in uniquePeptides):
prosolvePeptides.append(peptide)
if(len(prosolvePeptides) > 0 and len(percolatorPeptides) > 0):
if(verbose):
print "writing in " + str(OutputFile)
utils.writePeptides(prosolvePeptides,"peptides_prosolve_" + OutputFile)
else:
sys.stderr.write("the input file does not contain any information\n")
sys.exit()
if(verbose):
print "Prosolve file parsed"
if __name__ == "__main__":
main(sys.argv[1:])
percolatorPSMs = [
psm for psm in percolatorPSMs if psm.qvalue <= fdr
]
percolatorPeptides = [
pep for pep in percolatorPeptides if pep.qvalue <= fdr
]
percolatorProteins = [
prot for prot in percolatorProteins if prot.qvalue <= fdr
]
if (len(percolatorPSMs) > 0):
if (verbose):
print "writing in " + str(OutputFile)
utils.writePsms(percolatorPSMs, "psms_" + OutputFile)
if (len(percolatorPeptides) > 0):
utils.writePeptides(percolatorPeptides,
"peptides_" + OutputFile)
if (len(percolatorProteins) > 0):
utils.writeProteins(percolatorProteins,
"proteins_" + OutputFile)
else:
sys.stderr.write(
"the input file does not contain any information\n")
sys.exit()
if (verbose):
print "Percolator file parsed"
if __name__ == "__main__":
main(sys.argv[1:])
for line in f:
words = line.split()
prob = float(words[0])
sequence = str(words[1])
proteins = list(words[2:])
isdecoy = False
if (str(proteins[0]).find(decoy_pattern) != -1):
isdecoy = True
peptide = hit.Peptide(isdecoy, float(1 - prob), float(0.0),
float(0.0), float(0.0), str(sequence),
float(prob), [], proteins)
if (sequence in uniquePeptides):
prosolvePeptides.append(peptide)
if (len(prosolvePeptides) > 0 and len(percolatorPeptides) > 0):
if (verbose):
print "writing in " + str(OutputFile)
utils.writePeptides(prosolvePeptides,
"peptides_prosolve_" + OutputFile)
else:
sys.stderr.write(
"the input file does not contain any information\n")
sys.exit()
if (verbose):
print "Prosolve file parsed"
if __name__ == "__main__":
main(sys.argv[1:])
percolatorPeptides = per.getPeptides(elems)
percolatorProteins = per.getProteins(elems)
if(verbose):
print "Read " + str(len(percolatorPSMs)) + " PSMs"
print "Read " + str(len(percolatorPeptides)) + " Peptides"
print "Read " + str(len(percolatorProteins)) + " Proteins"
if(fdr < 1.0 and fdr > 0.0):
percolatorPSMs = [psm for psm in percolatorPSMs if psm.qvalue <= fdr]
percolatorPeptides = [pep for pep in percolatorPeptides if pep.qvalue <= fdr]
percolatorProteins = [prot for prot in percolatorProteins if prot.qvalue <= fdr]
if(len(percolatorPSMs) > 0):
if(verbose):
print "writing in " + str(OutputFile)
utils.writePsms(percolatorPSMs, "psms_" + OutputFile)
if(len(percolatorPeptides) > 0):
utils.writePeptides(percolatorPeptides,"peptides_" + OutputFile)
if(len(percolatorProteins) > 0):
utils.writeProteins(percolatorProteins,"proteins_" + OutputFile)
else:
sys.stderr.write("the input file does not contain any information\n")
sys.exit()
if(verbose):
print "Percolator file parsed"
if __name__ == "__main__":
main(sys.argv[1:])
tree2 = etree.parse(infile2,parser)
except Exception, inst:
sys.stderr.write("Unexpected error opening %s or %s: %s\n" % (infile,infile2, inst))
sys.exit()
if(verbose):
print "Reading " + str(argv[0])
print "Reading " + str(argv[1])
elems = tree.getroot()
elems2 = tree2.getroot()
tppPSMs,tppPeptides = tpp.readIprophetPSMsPeptides(elems,decoy_prefix)
tppProteins = tpp.readIprophetProteins(elems2,decoy_prefix)
if(len(tppPSMs) > 0 and len(tppPeptides) > 0 and len(tppProteins) > 0):
if(verbose):
print "writing in " + str(OutputFile)
utils.writePsms(tppPSMs, "psms_" + OutputFile)
utils.writePeptides(tppPeptides,"peptides_" + OutputFile)
utils.writeProteins(tppProteins,"proteins_" + OutputFile)
else:
sys.stderr.write("\nThe input files does not contain any information\n")
sys.exit()
if(verbose):
print "iProphet and Protein Prophet files parsed"
if __name__ == "__main__":
main(sys.argv[1:])
sys.exit()
if (verbose):
print "Reading " + str(argv[0])
print "Reading " + str(argv[1])
elems = tree.getroot()
elems2 = tree2.getroot()
tppPSMs, tppPeptides = tpp.readIprophetPSMsPeptides(
elems, decoy_prefix)
tppProteins = tpp.readIprophetProteins(elems2, decoy_prefix)
if (len(tppPSMs) > 0 and len(tppPeptides) > 0
and len(tppProteins) > 0):
if (verbose):
print "writing in " + str(OutputFile)
utils.writePsms(tppPSMs, "psms_" + OutputFile)
utils.writePeptides(tppPeptides, "peptides_" + OutputFile)
utils.writeProteins(tppProteins, "proteins_" + OutputFile)
else:
sys.stderr.write(
"\nThe input files does not contain any information\n")
sys.exit()
if (verbose):
print "iProphet and Protein Prophet files parsed"
if __name__ == "__main__":
main(sys.argv[1:])