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()
proteins_percolator= per.getProteins(elems)
peptides = per.getPeptides(elems)
ntarget_percolator = len([prot for prot in [prot for prot in proteins_percolator if not prot.isdecoy]])
ndecoy_percolator = len([prot for prot in [prot for prot in proteins_percolator if prot.isdecoy]])
print "Found " + str(ntarget_percolator) + " proteins"
print "doing parsimony at " + str(fdr)
parsimony_tmp = [prot for prot,pep in parsimony.getParsimony(peptides, fdr, True)]
ntarget_parsimony = len([prot for prot in parsimony_tmp if prot.find("random") == -1])
ndecoy_parsimony = len([prot for prot in parsimony_tmp if prot.find("random") != -1])
print "Found " + str(ntarget_parsimony) + " proteins at " + str(fdr) + " fdr doing parsimony"
print "Computed Gamma is " + str(float(ntarget_parsimony) / float(ntarget_percolator))
if __name__ == "__main__":
main(sys.argv[1:])
two_hit_thresholds_unique.append(fdr_2hit_unique)
print "Unique two peptide rule gives " + str(
ntarget_2peprule_unique) + " target proteins and " + str(
ndecoy_2peprule_unique) + " decoy proteins and " + str(
fdr_2hit_unique) + " qvalue"
if (maxtarget < ntarget_2peprule_unique):
maxtarget = ntarget_2peprule_unique
if (maxdecoy < ndecoy_2peprule_unique):
maxdecoy = ndecoy_2peprule_unique
print "doing parsimony at " + str(t)
parsimony_tmp = [
prot
for prot, pep in parsimony.getParsimony(peptides, t, qvalue)
]
ntarget_parsimony = len(
[prot for prot in parsimony_tmp if prot.find("random") == -1])
ndecoy_parsimony = len(
[prot for prot in parsimony_tmp if prot.find("random") != -1])
parsimony_proteins_target.append(ntarget_parsimony)
parsimony_proteins_decoy.append(ndecoy_parsimony)
if (num_targets_mayus > 0):
tmp_target = float(ntarget_parsimony) / float(
num_targets_mayus)
else:
tmp_target = 0
if (num_decoys_mayus > 0):
if(tmp_target > 0):
fdr_2hit_unique = float((tmp_decoy / tmp_target) * prot_fdr_mayus)
else:
fdr_2hit_unique = 0
two_hit_thresholds_unique.append(fdr_2hit_unique)
print "Unique two peptide rule gives " + str(ntarget_2peprule_unique) + " target proteins and " + str(ndecoy_2peprule_unique) + " decoy proteins and " +str(fdr_2hit_unique) + " qvalue"
if(maxtarget < ntarget_2peprule_unique):
maxtarget = ntarget_2peprule_unique
if(maxdecoy < ndecoy_2peprule_unique):
maxdecoy = ndecoy_2peprule_unique
print "doing parsimony at " + str(t)
parsimony_tmp = [prot for prot,pep in parsimony.getParsimony(peptides, t, qvalue)]
ntarget_parsimony = len([prot for prot in parsimony_tmp if prot.find("random") == -1])
ndecoy_parsimony = len([prot for prot in parsimony_tmp if prot.find("random") != -1])
parsimony_proteins_target.append(ntarget_parsimony)
parsimony_proteins_decoy.append(ndecoy_parsimony)
if(num_targets_mayus > 0 ):
tmp_target = float(ntarget_parsimony) / float(num_targets_mayus)
else:
tmp_target = 0
if(num_decoys_mayus > 0 ):
tmp_decoy = float(ndecoy_parsimony) / float(num_decoys_mayus)
else:
tmp_decoy = 0