def main(argv):
if (len(argv) < 1):
sys.stderr.write("Error: Number of arguments incorrect\n")
usage()
sys.exit()
else:
OutputFile = "output_fido.txt"
decoy_prefix = ""
verbose = False
try:
opts, args = getopt.getopt(
sys.argv[2:], "o:p:hv",
["output=", "pattern=", "help", "verbose"])
except getopt.GetoptError, err:
# print help information and exit:
print str(
err) # will print something like "option -a not recognized"
usage()
sys.exit(2)
for o, a in opts:
if o == "-v":
verbose = True
elif o in ("-h", "--help"):
usage()
sys.exit()
elif o in ("-o", "--output"):
OutputFile = a
elif o in ("-p", "--pattern"):
decoy_prefix = a
else:
assert False, "unhandled option"
if (os.path.isfile(argv[0])):
infile = argv[0]
else:
sys.stderr.write("Error: file not found\n")
sys.exit()
if (verbose):
print "Reading " + str(argv[0])
fidoproteins = utils.readFidoOuput(infile, decoy_prefix)
if (len(fidoproteins) > 0):
if (verbose):
print "writing in " + str(OutputFile)
utils.writeProteins([v for k, v in fidoproteins.items()],
OutputFile)
else:
sys.stderr.write("the input file does not contain any information")
sys.exit()
if (verbose):
print "Fido file parsed"
def main(argv):
if( len(argv) < 1):
sys.stderr.write("Error: Number of arguments incorrect\n")
usage()
sys.exit()
else:
OutputFile = "output_fido.txt"
decoy_prefix = ""
verbose = False
try:
opts, args = getopt.getopt(sys.argv[2:], "o:p:hv", ["output=","pattern=", "help", "verbose"])
except getopt.GetoptError, err:
# print help information and exit:
print str(err) # will print something like "option -a not recognized"
usage()
sys.exit(2)
for o, a in opts:
if o == "-v":
verbose = True
elif o in ("-h", "--help"):
usage()
sys.exit()
elif o in ("-o", "--output"):
OutputFile = a
elif o in ("-p", "--pattern"):
decoy_prefix = a
else:
assert False, "unhandled option"
if(os.path.isfile(argv[0])):
infile = argv[0]
else:
sys.stderr.write("Error: file not found\n")
sys.exit()
if(verbose):
print "Reading " + str(argv[0])
fidoproteins = utils.readFidoOuput(infile,decoy_prefix)
if(len(fidoproteins) > 0):
if(verbose):
print "writing in " + str(OutputFile)
utils.writeProteins([v for k,v in fidoproteins.items()],OutputFile)
else:
sys.stderr.write("the input file does not contain any information")
sys.exit()
if(verbose):
print "Fido file parsed"
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:])
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:])
