class DeltaExtractor(object):
def __init__(self, path):
self.path = path
self.masterSpectrum = MasterSpectrum()
def createDeltaMasterSpectrum(self,
min_rel_intensity,
delta_func=calculate_Delta_by_ppm(20)):
up = 0
with mgf.read(self.path) as spectra:
for spectrum in spectra:
print(up)
up += 1
int_dic = spectrum['intensity array']
mz_dic = spectrum['m/z array']
rel_int = calculateRelativeIntensity(int_dic)
smallerArea = [(i, j) for i, j in zip(mz_dic, rel_int)
if j >= min_rel_intensity]
mz_dic = [i for i, j in smallerArea]
rel_int = [j for i, j in smallerArea]
for i in range(len(mz_dic) - 1, -1, -1):
for j in range(i - 1, -1, -1):
diff = mz_dic[i] - mz_dic[j]
p = Peak(diff, rel_int[j],
delta_func) # intensities are from lower peak
self.masterSpectrum.add(p, 0)
def exportCsv(self, output_path):
self.masterSpectrum.export_to_csv(output_path)
class PrecursorDeltaPeaksExtractor(object):
def __init__(self, path):
self.path = path
self.masterSpectrum = MasterSpectrum()
def createDeltaPrecursorMasterSpectrum(
self, delta_func=calculate_Delta_by_ppm(20)):
with mgf.read(self.path) as spectra:
for spectrum in spectra:
int_dic = spectrum['intensity array']
mz_dic = spectrum['m/z array']
chrg_spec = spectrum['params']['charge'][0]
precursor = calculatePrecursor(
mz=spectrum['params']['pepmass'][0], charge=chrg_spec)
rel_int = calculateRelativeIntensity(int_dic)
for m, i in zip(mz_dic, rel_int):
p = Peak(precursor - float(m), float(i), delta_func)
self.masterSpectrum.add(p, 0)
def exportCsv(self, output_path):
self.masterSpectrum.export_to_csv(output_path)
