Python load_mzid Examples

Example #1

File: run_demix_pipeline_Centroid.py Project: wj-zhang/DeMix

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',
                 'Tryp1mis_fixCaC_varOxM.txt'), '-d', args.db, '-s',
    centroidSpec, '-o', centroidSpec + '.mzid'
]
# Q-Exactive, HCD, trypsin, 10 ppm precursor tol.
cmd += '-t 10ppm -ti 0,0 -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', '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',

Example #2

cmd = [
    args.exe, '-in', args.topp, '-resource_file', args.trf, '-out_dir',
    args.out_dir
]
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 '

Example #3

File: run_demix_pipeline.py Project: naimrashid/DeMix

# '======= first pass MS-GF+ database searching '
centroidSpec = os.path.join(args.out_dir,  'TOPPAS_out', '004-PeakPickerHiRes-out', os.path.basename(args.mzml).replace('.gz', ''))
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', 'Tryp1mis_fixCaC_varOxM.txt'),
		'-d', args.db,
		'-s', centroidSpec,
		'-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,

Example #4

File: run_demix_pipeline_TOPP2.py Project: naimrashid/DeMix

open(args.trf, 'w').write(trf)

# '======= run TOPP workflow for peak picking and feature detection'
cmd = [	args.exe,
		'-in', args.topp,
	 	'-resource_file', args.trf,
		'-out_dir', args.out_dir ]
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 '