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]) elems = tree.getroot() percolatorPSMs = per.getPSMs(elems) if (len(percolatorPSMs) > 0): if (verbose): print "writing in " + str(mayuOutputFile) utils.writeMayuInput(percolatorPSMs, mayuOutputFile) else: sys.stderr.write("the input file does not contain any psm") sys.exit() if (verbose): print "Mayu file generated" if __name__ == "__main__": main(sys.argv[1:])
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]) 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 = [prot for prot in percolatorProteins if prot.qvalue <= fdr] if(len(percolatorPSMs) > 0): if(verbose):
(infile, inst)) sys.exit() if (verbose): print "Reading " + str(argv[0]) elems = tree.getroot() thresholds = [ 0.0015, 0.0025, 0.005, 0.0075, 0.01, 0.015, 0.020, 0.030, 0.050, 0.060, 0.075, 0.090, 0.1, 0.15, 0.2 ] proteins_percolator = per.getProteins(elems) peptides = per.getPeptides(elems) psms = per.getPSMs(elems) percolator_proteins_target = list() percolator_proteins_decoy = list() twohit_proteins_target = list() twohit_proteins_decoy = list() twohit_proteins_target_unique = list() twohit_proteins_decoy_unique = list() parsimony_proteins_target = list() parsimony_proteins_decoy = list() mayu_proteins_target = list() mayu_proteins_decoy = list() mayu_proteins_target_1psm = list() mayu_proteins_decoy_1psm = list() mayu_proteins_target_2psm = list()
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() thresholds = [0.0015,0.0025,0.005,0.0075,0.01,0.015,0.020,0.030,0.050,0.060,0.075,0.090,0.1,0.15,0.2] proteins_percolator= per.getProteins(elems) peptides = per.getPeptides(elems) psms = per.getPSMs(elems) percolator_proteins_target = list() percolator_proteins_decoy = list() twohit_proteins_target = list() twohit_proteins_decoy = list() twohit_proteins_target_unique = list() twohit_proteins_decoy_unique = list() parsimony_proteins_target = list() parsimony_proteins_decoy = list() mayu_proteins_target = list() mayu_proteins_decoy = list() mayu_proteins_target_1psm = list() mayu_proteins_decoy_1psm = list() mayu_proteins_target_2psm = list()