Python spectra_clone Exemples

Exemple #1

Fichier : run_demix_pipeline_Centroid.py Projet : wj-zhang/DeMix

)
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)

Exemple #2

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()

Exemple #3

Fichier : run_demix_pipeline.py Projet : naimrashid/DeMix

		'-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)

Exemple #4

Fichier : run_demix_pipeline_TOPP2.py Projet : naimrashid/DeMix

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)