def main(argv):
if( len(argv) < 2):
sys.stderr.write("Error: Number of arguments incorrect\n")
usage()
sys.exit()
else:
fidoOutputFile = "output.txt"
fidoDBfile = "db.txt"
verbose = False
decoy_prefix = "random"
m = 1
try:
opts, args = getopt.getopt(sys.argv[3:], "o:p:d:hvm:", ["output=", "pattern=", "database=", "help", "verbose", "max="])
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"):
fidoOutputFile = a
elif o in ("-p", "--pattern"):
decoy_prefix = a
elif o in ("-d", "--database"):
fidoDBfile = a
elif o in ("-m", "--max"):
m = int(a)
else:
assert False, "unhandled option"
if(os.path.isfile(argv[0]) and os.path.isfile(argv[1])):
target = argv[0]
decoy = argv[1]
else:
sys.stderr.write("Error: XML file not found\n")
sys.exit()
if(verbose):
print "Reading " + str(argv[0])
print "Reading " + str(argv[1])
targetPSMs = utils.parseSqt(target,m,False)
decoyPSMs = utils.parseSqt(decoy,m,True)
if(verbose):
print "read " + str(len(targetPSMs)) + " target PSMs"
print "read " + str(len(decoyPSMs)) + " decoy PSMs"
##run qvality
tmp_file_target = "qvality_tmp_target.txt"
tmp_file_decoy = "qvality_tmp_decoy.txt"
tmp_qvality = "qvality_tmp.txt"
targetPSMs = sorted(targetPSMs,key=attrgetter('score'),reverse=True)
decoyPSMs = sorted(decoyPSMs,key=attrgetter('score'),reverse=True)
PSMs = targetPSMs + decoyPSMs
PSMs = sorted(PSMs,key=attrgetter('score'),reverse=True)
target_file = open(tmp_file_target,"w")
for target_psm in targetPSMs:
target_file.write(str(target_psm.score) + "\n")
target_file.close()
decoy_file = open(tmp_file_decoy,"w")
for decoy_psm in decoyPSMs:
decoy_file.write(str(decoy_psm.score) + "\n")
decoy_file.close()
command = "qvality -d -o " + "\"" + str(tmp_qvality) + "\" " + str(tmp_file_target) + " " + str(tmp_file_decoy) + " "
if(verbose):
print command
retcode = os.system(command)
if(retcode != 0):
sys.stderr.write("Error: executing qvality\n")
sys.exit()
if(not verbose):
os.remove(tmp_file_decoy)
os.remove(tmp_file_target)
results_qvality = open(tmp_qvality,"r").readlines()
results_qvality.pop(0)
if( len(results_qvality) != len(PSMs) ):
sys.stderr.write("the results from qvality contain less rows than the read PSMs\n")
sys.exit()
else:
for i in xrange(0,len(results_qvality)):
row = results_qvality[i]
words = row.split()
score = float(words[0])
pep = float(words[1])
qvalue = float(words[2])
if(score != round(PSMs[i].score,len(str(score).split(".")[1])) ):
sys.stderr.write("The score of PSM : " + str(PSMs[i].name) + " is " + str(PSMs[i].score) + " and does not correspond to the score read from qvality that is " +str(score) + "\n")
else:
PSMs[i].pep = pep
PSMs[i].qvalue = qvalue
if(not verbose):
os.remove(tmp_qvality)
utils.writeFidoInput(PSMs, fidoOutputFile, fidoDBfile, decoy_prefix)
if(verbose):
print "done"
def main(argv):
if (len(argv) < 2):
sys.stderr.write("Error: Number of arguments incorrect\n")
usage()
sys.exit()
else:
fidoOutputFile = "output.txt"
fidoDBfile = "db.txt"
verbose = False
decoy_prefix = "random"
m = 1
try:
opts, args = getopt.getopt(sys.argv[3:], "o:p:d:hvm:", [
"output=", "pattern=", "database=", "help", "verbose", "max="
])
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"):
fidoOutputFile = a
elif o in ("-p", "--pattern"):
decoy_prefix = a
elif o in ("-d", "--database"):
fidoDBfile = a
elif o in ("-m", "--max"):
m = int(a)
else:
assert False, "unhandled option"
if (os.path.isfile(argv[0]) and os.path.isfile(argv[1])):
target = argv[0]
decoy = argv[1]
else:
sys.stderr.write("Error: XML file not found\n")
sys.exit()
if (verbose):
print "Reading " + str(argv[0])
print "Reading " + str(argv[1])
targetPSMs = utils.parseSqt(target, m, False)
decoyPSMs = utils.parseSqt(decoy, m, True)
if (verbose):
print "read " + str(len(targetPSMs)) + " target PSMs"
print "read " + str(len(decoyPSMs)) + " decoy PSMs"
##run qvality
tmp_file_target = "qvality_tmp_target.txt"
tmp_file_decoy = "qvality_tmp_decoy.txt"
tmp_qvality = "qvality_tmp.txt"
targetPSMs = sorted(targetPSMs, key=attrgetter('score'), reverse=True)
decoyPSMs = sorted(decoyPSMs, key=attrgetter('score'), reverse=True)
PSMs = targetPSMs + decoyPSMs
PSMs = sorted(PSMs, key=attrgetter('score'), reverse=True)
target_file = open(tmp_file_target, "w")
for target_psm in targetPSMs:
target_file.write(str(target_psm.score) + "\n")
target_file.close()
decoy_file = open(tmp_file_decoy, "w")
for decoy_psm in decoyPSMs:
decoy_file.write(str(decoy_psm.score) + "\n")
decoy_file.close()
command = "qvality -d -o " + "\"" + str(tmp_qvality) + "\" " + str(
tmp_file_target) + " " + str(tmp_file_decoy) + " "
if (verbose):
print command
retcode = os.system(command)
if (retcode != 0):
sys.stderr.write("Error: executing qvality\n")
sys.exit()
if (not verbose):
os.remove(tmp_file_decoy)
os.remove(tmp_file_target)
results_qvality = open(tmp_qvality, "r").readlines()
results_qvality.pop(0)
if (len(results_qvality) != len(PSMs)):
sys.stderr.write(
"the results from qvality contain less rows than the read PSMs\n"
)
sys.exit()
else:
for i in xrange(0, len(results_qvality)):
row = results_qvality[i]
words = row.split()
score = float(words[0])
pep = float(words[1])
qvalue = float(words[2])
if (score != round(PSMs[i].score, len(
str(score).split(".")[1]))):
sys.stderr.write(
"The score of PSM : " + str(PSMs[i].name) + " is " +
str(PSMs[i].score) +
" and does not correspond to the score read from qvality that is "
+ str(score) + "\n")
else:
PSMs[i].pep = pep
PSMs[i].qvalue = qvalue
if (not verbose):
os.remove(tmp_qvality)
utils.writeFidoInput(PSMs, fidoOutputFile, fidoDBfile, decoy_prefix)
if (verbose):
print "done"
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()
percolatorPeptides = per.getPeptides(elems)
percolatorPSMs = per.getPSMs(elems)
if(len(percolatorPSMs) > 0):
if(verbose):
print "writing in " + str(fidoOutputFile)
utils.writeFidoInput(percolatorPSMs,"psms_" + fidoOutputFile,fidoDBfile,decoy_prefix)
if(len(percolatorPeptides) > 0):
utils.writeFidoInput(percolatorPeptides,"peptides_" + fidoOutputFile,fidoDBfile,decoy_prefix)
else:
sys.stderr.write("the input file does not contain any peptide or psms\n")
sys.exit()
if(verbose):
print "Fido file generated"
if __name__ == "__main__":
main(sys.argv[1:])
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()
percolatorPeptides = per.getPeptides(elems)
percolatorPSMs = per.getPSMs(elems)
if (len(percolatorPSMs) > 0):
if (verbose):
print "writing in " + str(fidoOutputFile)
utils.writeFidoInput(percolatorPSMs, "psms_" + fidoOutputFile,
fidoDBfile, decoy_prefix)
if (len(percolatorPeptides) > 0):
utils.writeFidoInput(percolatorPeptides,
"peptides_" + fidoOutputFile, fidoDBfile,
decoy_prefix)
else:
sys.stderr.write(
"the input file does not contain any peptide or psms\n")
sys.exit()
if (verbose):
print "Fido file generated"
if __name__ == "__main__":
main(sys.argv[1:])
else:
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()
tppPSMs,tppPeptides = tpp.readIprophetPSMsPeptides(elems,prefix)
if(len(tppPSMs) > 0):
if(verbose):
print "writing in " + str(fidoOutputFile)
utils.writeFidoInput(tppPSMs,fidoOutputFile,fidoDBfile,prefix)
else:
sys.stderr.write("the input file does not contain any peptide or psms\n")
sys.exit()
if(verbose):
print "Fido file generated"
if __name__ == "__main__":
main(sys.argv[1:])
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()
tppPSMs, tppPeptides = tpp.readIprophetPSMsPeptides(elems, prefix)
if (len(tppPSMs) > 0):
if (verbose):
print "writing in " + str(fidoOutputFile)
utils.writeFidoInput(tppPSMs, fidoOutputFile, fidoDBfile, prefix)
else:
sys.stderr.write(
"the input file does not contain any peptide or psms\n")
sys.exit()
if (verbose):
print "Fido file generated"
if __name__ == "__main__":
main(sys.argv[1:])