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()
