def write_mzml(file_name, spectra, title_prefix='Spectrum ', output_dir='./'):
if '.mzml' not in file_name.lower():
file_name += '.mzML'
output_file = output_dir + file_name
exp = MSExperiment()
sp_count = 0
for spectrum in spectra:
spec = MSSpectrum()
spec.setMSLevel(2)
name = str.encode(title_prefix + str(sp_count))
spec.setName(name)
sp_count += 1
i = [500 for _ in spectrum['spectrum']]
spec.set_peaks([spectrum['spectrum'], i])
spec.setMSLevel(2)
prec = Precursor()
prec.setCharge(2)
prec.setMZ(spectrum['precursor_mass'])
spec.setPrecursors([prec])
spec.sortByPosition()
exp.addSpectrum(spec)
MzMLFile().store(output_file, exp)
return output_file
def read_ms1_experiment(filepath):
source_experiment = MSExperiment()
file_handler = FileHandler()
# bytes is required by `loadExperiment()` called below
typed_fp = filepath if isinstance(filepath, bytes) else filepath.encode()
file_handler.loadExperiment(typed_fp, source_experiment)
ms1_experiment = MSExperiment()
for spectrum in source_experiment:
if spectrum.getMSLevel() == 1:
ms1_experiment.addSpectrum(spectrum)
return ms1_experiment
def read_ms1_experiment(filepath):
# pylint: disable=import-outside-toplevel,no-name-in-module,import-error
from pyopenms import FileHandler, MSExperiment
source_experiment = MSExperiment()
file_handler = FileHandler()
# bytes is required by `loadExperiment()` called below
typed_fp = filepath if isinstance(filepath,
bytes) else filepath.encode()
file_handler.loadExperiment(typed_fp, source_experiment)
ms1_experiment = MSExperiment()
for spectrum in source_experiment:
if spectrum.getMSLevel() == 1:
ms1_experiment.addSpectrum(spectrum)
return ms1_experiment
def write_mzml(file_name, spectra, title_prefix='Spectrum ', output_dir='./'):
if '.mzml' not in file_name.lower():
file_name += '.mzML'
output_file = output_dir + file_name
exp = MSExperiment()
sp_count = 0
ids = {}
tic = []
for spectrum in spectra:
spec = MSSpectrum()
spec.setMSLevel(2)
name = title_prefix + str(
sp_count) if 'name' not in spectrum else spectrum['name']
ids[sp_count] = name
sp_count += 1
if 'abundance' not in spectrum:
print('oops')
i = [500 for _ in spectrum['spectrum']]
else:
i = spectrum['abundance']
tic.append(sum(i))
spec.set_peaks([spectrum['spectrum'], i])
spec.setMSLevel(2)
prec = Precursor()
# check to see if a precursor charge was provided
pc = 2 if 'precursor_charge' not in spectrum else spectrum[
'precursor_charge']
prec.setCharge(pc)
prec.setMZ(spectrum['precursor_mass'])
spec.setPrecursors([prec])
spec.sortByPosition()
exp.addSpectrum(spec)
MzMLFile().store(output_file, exp)
# load it back and fix it
tree = ET.parse(output_file)
mzml = tree.find('{http://psi.hupo.org/ms/mzml}mzML')
# add an id to the mzml
mzml.set('id', 'testSpectraFileFixed')
mzml.set('xmlns', "http://psi.hupo.org/ms/mzml")
mzml.set('xmlns:xsi', 'http://www.w3.org/2001/XMLSchema-instance')
# remove some info from the mzml header [accession, version]
toDelMzml = ['accession']
for todel in toDelMzml:
del mzml.attrib[todel]
# add file description stuff to the fileDescription tag
fileDescription = mzml.find('{http://psi.hupo.org/ms/mzml}fileDescription')
sourceFileElement = ET.fromstring(
'<sourceFileList count="1"> <sourceFile id="NOD2_E3.mzXML" name="NOD2_E3.mzXML" location="file:///C:/Users/zachmcgrath/Downloads"> <cvParam cvRef="MS" accession="MS:1000776" name="scan number only nativeID format" value=""/> <cvParam cvRef="MS" accession="MS:1000566" name="ISB mzXML format" value=""/> <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="89ecb0dd31ca3a2fdf5ef2c4f5341f6e5e9f06f0"/> </sourceFile> </sourceFileList>'
)
fileDescription.append(sourceFileElement)
instrumentConfigurationList = mzml.find(
'{http://psi.hupo.org/ms/mzml}instrumentConfigurationList')
instrumentConfiguration = ET.fromstring(
' <instrumentConfiguration id="IC1"> <componentList count="3"> <source order="1"> <userParam name="msIonisation" value="HPLC-Chip/MS"/> </source> <analyzer order="1"> <userParam name="msMassAnalyzer" value="Q-TOF"/> </analyzer> <detector order="1"> <userParam name="msDetector" value="ADC"/> </detector> </componentList> </instrumentConfiguration>'
)
for child in instrumentConfigurationList:
del child
instrumentConfigurationList.append(instrumentConfiguration)
run = mzml.find('{http://psi.hupo.org/ms/mzml}run')
spectrumList = run.find('{http://psi.hupo.org/ms/mzml}spectrumList')
print(len(spectrumList))
for i, spectrumElement in enumerate(spectrumList):
# set the id
spectrumElement.set('id', ids[i])
# need to add this
# <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
centroidElement = ET.Element('{http://psi.hupo.org/ms/mzml}cvParam',
attrib={
'name': 'centroid spectrum',
'accession': 'MS:1000127',
'value': ''
})
pl = spectrumElement.find('{http://psi.hupo.org/ms/mzml}precursorList')
bdal = spectrumElement.find(
'{http://psi.hupo.org/ms/mzml}binaryDataArrayList')
if bdal is None or pl is None:
print(spectrumElement)
spectrumList.remove(spectrumElement)
# add the range. Not good for MSConvert for whatever reason
scanListEl = spectrumElement.find(
'{http://psi.hupo.org/ms/mzml}scanList')
scanEl = scanListEl.find('{http://psi.hupo.org/ms/mzml}scan')[0]
scanWindowListElement = ET.fromstring(
'<scanWindowList count="1"> <scanWindow> <cvParam cvRef="MS" accession="MS:1000501" value="0" name="scan window lower limit" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" /> <cvParam cvRef="MS" accession="MS:1000500" value="10000" name="scan window upper limit" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" /> </scanWindow></scanWindowList>'
)
scanEl.append(scanWindowListElement)
spectrumElement.append(centroidElement)
timearray = base64.encodebytes(
struct.pack(f'<{len(tic)}f', *[i + 1 for i in range(len(tic))]))
ticarray = base64.encodebytes(struct.pack(f'<{len(tic)}f', *tic))
chromatogramListElmentString = f' <chromatogramList count="1" defaultDataProcessingRef="mzLibProcessing"> <chromatogram id="TIC" index="0" defaultArrayLength="1025" dataProcessingRef="mzLibProcessing"> <cvParam cvRef="MS" accession="MS:1000235" value="" name="total ion current chromatogram" /> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="10936"> <cvParam cvRef="MS" accession="MS:1000523" value="" name="64-bit float" /> <cvParam cvRef="MS" accession="MS:1000576" value="" name="no compression" /> <cvParam cvRef="MS" accession="MS:1000595" value="" name="time array" unitAccession="UO:0000031" unitName="Minutes" unitCvRef="UO" /> <binary>{timearray}</binary> </binaryDataArray> <binaryDataArray encodedLength="10936"> <cvParam cvRef="MS" accession="MS:1000523" value="" name="64-bit float" /> <cvParam cvRef="MS" accession="MS:1000576" value="" name="no compression" /> <cvParam cvRef="MS" accession="MS:1000515" value="" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS" /> <binary>{ticarray}</binary> </binaryDataArray> </binaryDataArrayList> </chromatogram> </chromatogramList>'
chromatogramListElment = ET.fromstring(chromatogramListElmentString)
run.append(chromatogramListElment)
tree.write(output_file, encoding='utf-8', xml_declaration=True)
return output_file
def combine_experiments(exp1: ms.MSExperiment, exp2: ms.MSExperiment) -> None:
"""Merges two experiments (putting the second into the first)."""
for i in range(exp2.getNrSpectra()):
spec = exp2.getSpectrum(i)
exp1.addSpectrum(spec)