sys.exit()
parser = etree.XMLParser(ns_clean=False, huge_tree=True)
try:
tree = etree.parse(infile,parser)
except Exception, inst:
sys.stderr.write("Unexpected error opening %s: %s\n" % (infile, inst))
sys.exit()
if(verbose):
print "Reading " + str(argv[0])
elems = tree.getroot()
##READING ELEMENTS##
peptides = per.getPeptides(elems)
print "Read " + str(len(peptides)) + " peptides"
if(qvalue):
peptides = [peptide for peptide in peptides if peptide.qvalue <= float(fdr)]
else:
peptides = [peptide for peptide in peptides if peptide.pep <= float(fdr)]
print "There are " + str(len(peptides)) + " peptides at " +str(fdr) + " threshold"
proteins_filter = getProteins(peptides)
proteins_filter_unique = getProteinsUnique(peptides)
print "\nWriting results to " + outfile
outf = open(outfile, "w")
outf2 = open("unique_" + outfile, "w")
outf.write("Protein\tProbability\tPeptides\n")
outf2.write("Protein\tProbability\tPeptides\n")
for protein in proteins_filter:
sys.stderr.write("Error: XML file not found\n")
sys.exit()
parser = etree.XMLParser(ns_clean=False, huge_tree=True)
try:
tree = etree.parse(infile,parser)
except Exception, inst:
sys.stderr.write("Unexpected error opening %s: %s\n" % (infile, inst))
sys.exit()
if(verbose):
print "Reading " + str(argv[0])
print "Reading " + str(argv[1])
elems = tree.getroot()
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)
parser = etree.XMLParser(ns_clean=False, huge_tree=True)
try:
tree = etree.parse(infile, parser)
except Exception, inst:
sys.stderr.write("Unexpected error opening %s: %s\n" %
(infile, inst))
sys.exit()
if (verbose):
print "Reading " + str(argv[0])
elems = tree.getroot()
percolatorPSMs = per.getPSMs(elems)
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 = [