def spectrumDescriptionToMZ(description):
if 'MultiplierzMGF' in description:
return float(standard_title_parse(description)['mz'])
try:
return float(description.split('-|')[0].split('-')[-1])
except ValueError:
return float(description.split("|")[1])
def mgf_to_ms2(mgfFile, outputfile=None):
"""
Converts the commonly-used MGF format to an MS2 file.
"""
if not outputfile:
outputfile = mgfFile[:-4] + '.ms2'
mgf = parse_mgf(mgfFile, header=False)
ms2 = MS2Writer(outputfile,
date=time.localtime(),
extractor='Converted from MGF by Multiplierz',
extractorVersion=__version__,
extractorOptions="None")
sampleTitle = mgf.values()[0]['title']
if 'MultiplierzMGF' in sampleTitle:
titleMode = 'standard'
elif sampleTitle.count('.') > 2 and sampleTitle.split(
'.')[1] == sampleTitle.split('.')[2] and '|' in sampleTitle:
titleMode = 'classic' # From that old, barbaric format.
else:
titleMode = 'mysterious!'
print "WARNING: Spectrum title format not recognized; original spectrum numbering will be lost!"
scanNum = 0
for entry in mgf.values():
if titleMode == 'standard':
info = standard_title_parse(entry['title'])
scanNum = info['scan']
elif titleMode == 'classic':
scanNum = entry['title'].split('.')[1]
else:
scanNum += 1
ms2.write(
entry['spectrum'],
scanNum=scanNum,
charge=entry.get('charge',
0), # TODO Add default charge to PyComet?
precursorMZ=entry['pepmass'])
ms2.close()
return outputfile
def spectrumDescriptionToScanNumber(description):
if 'MultiplierzMGF' in description:
return int(standard_title_parse(description)['scan'])
else:
return int(description.split('.')[1])
def _getReporters(row):
attrib = standard_title_parse(row['Spectrum Description'])
return [float(attrib[x.lower()]) for x in isobaric_labels[isobaric]]