#
# Make smaller mzXML file to keep in repo
#
n_spectra_to_keep = 20
exp = MSExperiment()
MzXMLFile().load(mzXML_file, exp)
print(f"Full size of experiment {len(exp.getSpectra())}")
spec = []
for i, s in enumerate(exp.getSpectra()):
if i == n_spectra_to_keep:
break
spec.append(s)
exp.setSpectra(spec)
print(f"New size of experiment {len(exp.getSpectra())}")
MzXMLFile().store("test.mzXML", exp)
#
# Take subset of CSV LabView data
#
cols = ["time", "b", "temp", "d", "e", "f", "g", "h"]
df = pd.read_csv(labview_file, names=cols)
df["time"] -= df["time"][0]
df = df[:n_spectra_to_keep * 2 + 2]
# Ideally we'd keep the header, but by not we show people how to enter the columns
df.to_csv("test.csv", header=False)
def load(self, ifname: str, peakMap: pyopenms.MSExperiment):
inF = open(ifname, 'r')
lines = inF.read().splitlines()
curLine = 0
nLines = len(lines)
#generate spectrum list
spectraList = list()
while curLine < nLines:
if lines[curLine] == 'BEGIN IONS':
spectrum = pyopenms.MSSpectrum()
spectrum.setMSLevel(2)
precursor = pyopenms.Precursor()
curLine += 1
while curLine < nLines:
if lines[curLine][0].isalpha():
match = re.search('^([A-Z]+)=(.+)$', lines[curLine])
if match.group(1) == 'TITLE':
titleData = match.group(2).split(',')
for s in titleData:
if re.search('^scan[_=]', s):
match = re.search('^scan[_=]([0-9]+)', s)
assert (len(match.groups()) == 1)
spectrum.setNativeID('scan={}'.format(
match.group(1)))
elif match.group(1) == 'PEPMASS':
preMZ = [
float(x) for x in match.group(2).split(' ')
]
assert (len(preMZ) <= 2)
precursor.setMZ(preMZ[0])
if len(preMZ) > 1:
precursor.setIntensity(preMZ[1])
elif match.group(1) == 'CHARGE':
match = re.search('^([0-9])[+-]{0,1}$',
match.group(2))
assert (len(match.groups()) == 1)
precursor.setCharge(int(match.group(1)))
elif match.group(1) == 'RTINSECONDS':
spectrum.setRT(float(match.group(2)))
elif lines[curLine][0].isnumeric():
while curLine < nLines and lines[curLine] != 'END IONS':
ion = [float(x) for x in lines[curLine].split(' ')]
assert (len(ion) == 2)
ion_temp = pyopenms.Peak1D()
ion_temp.setMZ(ion[0])
ion_temp.setIntensity(ion[1])
spectrum.push_back(ion_temp)
curLine += 1
break
curLine += 1
spectrum.setPrecursors([precursor])
spectraList.append(spectrum)
curLine += 1
peakMap.setSpectra(spectraList)