) print ' '.join(cmd) subprocess.call(cmd) # '======== DeMix ' macc, max_scan = feature_ms2_clone.load_mzid(centroidSpec + '.mzid', qval=0.005) t = macc.std() * 3 t = t > 10 and 10 or t demixSpec = centroidSpec + '.demix.mgf' featureTab = os.path.join( args.out_dir, 'TOPPAS_out', '006-TextExporter', os.path.basename(args.mzml).replace('.gz', '').replace('.mzML', '.csv')) demixSpec = feature_ms2_clone.spectra_clone(featureTab, centroidSpec, macc.mean(), max_scan, float(args.w)) # '======== second pass MS-GF+ dababase search ' cmd = [ 'java', '-Xmx8g', '-jar', os.path.join(os.path.dirname(args.topp), 'MSGFPlus', 'MSGFPlus.jar'), '-mod', os.path.join(os.path.dirname(args.topp), 'MSGFPlus', 'Tryp2mis_fixCaC_varOxM_AcProtN_DaNQ.txt'), '-d', args.db, '-s', demixSpec, '-o', demixSpec + '.mzid', '-t', '%.1fppm' % t ] # adaptive mass tolerance # Q-Exactive, HCD, trypsin 2 missed, 0/1 13C cmd += '-ti 0,1 -m 3 -inst 3 -minLength 7 -addFeatures 1 -tda 1'.split() print ' '.join(cmd)
msgfout = os.path.join(args.out_dir, 'TOPPAS_out', '008-MSGFPlusAdapter-mzid_out', os.path.basename(args.mzml).replace('.gz', '')) # '======== DeMix ' macc, max_scan = feature_ms2_clone.load_mzid(msgfout + '.mzid', qval=0.005) t = macc.std() * 3 t = t > 10 and 10 or t featureTab = os.path.join( args.out_dir, 'TOPPAS_out', '013-TextExporter-out', os.path.basename(args.mzml).replace('.gz', '').replace('.mzML', '.csv')) demixSpec = feature_ms2_clone.spectra_clone( feature_fn=featureTab, mzml_fn=centroidSpec, dm_offset=macc.mean(), max_scan=max_scan, full_iso_width=float(args.w), out_dir=os.path.dirname(centroidSpec)) # '======== second pass MS-GF+ dababase search ' cmd = [ 'java', '-Xmx8g', '-jar', os.path.join(os.path.dirname(args.topp), 'MSGFPlus', 'MSGFPlus.jar'), '-mod', os.path.join(os.path.dirname(args.topp), 'MSGFPlus', 'Tryp2mis_fixCaC_varOxM_AcProtN_DaNQ.txt'), '-d', args.db, '-s', demixSpec, '-o', demixSpec + '.mzid', '-t', '%.1fppm' % t ] # adaptive mass tolerance cmd += '-ti 0,1 -m 3 -inst 3 -minLength 7 -addFeatures 1 -tda 1'.split()
'-o', centroidSpec + '.mzid' ] # Q-Exactive, HCD, trypsin, 0/1 13C, 10 ppm precursor tol. cmd += '-t 10ppm -ti 0,1 -m 3 -inst 3 -minLength 7 -addFeatures 1 -tda 1'.split() print ' '.join(cmd) subprocess.call(cmd) # '======== DeMix ' macc, max_scan = feature_ms2_clone.load_mzid(centroidSpec + '.mzid', qval=0.005) t = macc.std() * 3 t = t > 10 and 10 or t demixSpec = centroidSpec + '.demix.mgf' featureTab = os.path.join(args.out_dir, 'TOPPAS_out', '009-TextExporter-out', os.path.basename(args.mzml).replace('.gz', '').replace('.mzML', '.csv')) demixSpec = feature_ms2_clone.spectra_clone( featureTab, centroidSpec, macc.mean(), max_scan, float(args.w)) # '======== second pass MS-GF+ dababase search ' cmd = [ 'java', '-Xmx8g', '-jar', os.path.join(os.path.dirname(args.topp), 'MSGFPlus', 'MSGFPlus.jar'), '-mod', os.path.join(os.path.dirname(args.topp), 'MSGFPlus', 'Tryp2mis_fixCaC_varOxM_AcProtN_DaNQ.txt'), '-d', args.db, '-s', demixSpec, '-o', demixSpec + '.mzid', '-t', '%.1fppm' % t] # adaptive mass tolerance cmd += '-ti 0,1 -m 3 -inst 3 -minLength 7 -addFeatures 1 -tda 1'.split() print ' '.join(cmd) subprocess.call(cmd)
centroidSpec = os.path.join(args.out_dir, 'TOPPAS_out', '006-PeakPickerHiRes-out', os.path.basename(args.mzml).replace('.gz', '')) msgfout = os.path.join(args.out_dir, 'TOPPAS_out', '008-MSGFPlusAdapter-mzid_out', os.path.basename(args.mzml).replace('.gz', '')) # '======== DeMix ' macc, max_scan = feature_ms2_clone.load_mzid(msgfout + '.mzid', qval=0.005) t = macc.std() * 3 t = t > 10 and 10 or t featureTab = os.path.join(args.out_dir, 'TOPPAS_out', '013-TextExporter-out', os.path.basename(args.mzml).replace('.gz', '').replace('.mzML', '.csv')) demixSpec = feature_ms2_clone.spectra_clone( feature_fn = featureTab, mzml_fn = centroidSpec, dm_offset = macc.mean(), max_scan = max_scan, full_iso_width = float(args.w), out_dir = os.path.dirname(centroidSpec)) # '======== second pass MS-GF+ dababase search ' cmd = [ 'java', '-Xmx8g', '-jar', os.path.join(os.path.dirname(args.topp), 'MSGFPlus', 'MSGFPlus.jar'), '-mod', os.path.join(os.path.dirname(args.topp), 'MSGFPlus', 'Tryp2mis_fixCaC_varOxM_AcProtN_DaNQ.txt'), '-d', args.db, '-s', demixSpec, '-o', demixSpec + '.mzid', '-t', '%.1fppm' % t] # adaptive mass tolerance cmd += '-ti 0,1 -m 3 -inst 3 -minLength 7 -addFeatures 1 -tda 1'.split() print ' '.join(cmd)