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"
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:])
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:])
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:])