import re
import pepxml
usage_mesg = 'Usage: TPP-pep-xml2hit_list.py <PeptideProphet .xml file>'
if (len(sys.argv) != 2):
print usage_mesg
sys.exit(1)
filename_pepxml = sys.argv[1]
if (not os.access(filename_pepxml, os.R_OK)):
print "%s is not accessible." % filename_pepxml
print usage_mesg
sys.exit(1)
PSM = pepxml.parse_by_filename(filename_pepxml)
filename_out = filename_pepxml.replace('.pepxml', '').replace('.xml',
'') + '.hit_list'
sys.stderr.write("Write %s ... \n" % filename_out)
f_out = open(filename_out, 'w')
f_out.write("# pepxml: %s\n" % filename_pepxml)
f_out.write(
"#Spectrum_id\tCharge\tNeutralMass\tPeptide\tProtein\tMissedCleavages\tAbsScore(Xcorr)\tRelScore(DeltaCn)\tProbability\n"
)
f_out95 = open(filename_out + "_P095", 'w')
f_out95.write("# pepxml: %s\n" % filename_pepxml)
f_out95.write(
"#Spectrum_id\tCharge\tNeutralMass\tPeptide\tProtein\tMissedCleavages\tAbsScore(Xcorr)\tRelScore(DeltaCn)\tProbability\n"
)
for spectrum_id in PSM.keys():
import re
import pepxml
usage_mesg = 'Usage: myrimatch_pepxml-to-mvh_hit_list.py <.pepxml file>'
if( len(sys.argv) != 2 ):
print usage_mesg
sys.exit(1)
filename_pepxml = sys.argv[1]
if( not os.access(filename_pepxml,os.R_OK) ):
print "%s is not accessible."%filename_pepxml
print usage_mesg
sys.exit(1)
PSM = pepxml.parse_by_filename(filename_pepxml)
filename_out = filename_pepxml
filename_out = re.sub('.pepxml$','',filename_out)
filename_out += '.mvh_hit_list'
sys.stderr.write("Write %s ... \n"%filename_out)
f_out = open(filename_out,'w')
f_out.write("# pepxml: %s\n"%filename_pepxml)
f_out.write("#Spectrum_id\tCharge\tPrecursorMz\tMassDiff\tPeptide\tProtein\tMissedCleavages\tScore(mvh)\n")
for spectrum_id in PSM.keys():
charge = PSM[spectrum_id]['charge']
precursor_mz = PSM[spectrum_id]['precursor_mz']
best_peptide = ''
best_protein = ''
best_mvh = -100
best_mzMAE = 0