def extract_peaks(file,time_range):
peak_data = {}
run = pymzml.run.Reader(file)
peak_data[file] = {}
print(file)
for spec in run:
if spec.get('filter string')!= None and spec.get('total ion current') != None and spec.get('scan time') >= time_range[0] and spec.get('scan time') <= time_range[1]:
if spec.get('filter string') in peak_data[file]:
peak_data[file][spec.get('filter string')]['scan_count'] += 1
peak_data[file][spec.get('filter string')]['scan'] = mspy.combine(peak_data[file][spec.get('filter string')]['scan'], np.array(spec.peaks))
else:
peak_data[file][spec.get('filter string')] = {}
peak_data[file][spec.get('filter string')]['scan_count'] = 1
peak_data[file][spec.get('filter string')]['scan'] = np.array(spec.peaks)
for scan in peak_data[file].keys():
peak_data[file][scan]['scan'] = mspy.reduce(peak_data[file][scan]['scan'])
peak_data[file][scan]['scan'] = mspy.multiply(peak_data[file][scan]['scan'],y=1.0/peak_data[file][scan]['scan_count'])
with open(file+scan+'.np', 'wb') as f:
np.save(f,peak_data[file][scan]['scan'])
def integrate_match_data(self):
# Creates peptide inensities dictionary with timeline of intensities
# and sum of intensities for all charge states for each peptide
self.peptide_intensities = {}
self.peptide_intensities_int = {}
# Preparing data structures
for peptide in self.matched_peptides.keys():
self.peptide_intensities[peptide] = {}
self.peptide_intensities_int[peptide] = 0.0
for z in self.matched_peptides[peptide].keys():
self.peptide_intensities[peptide][z] = []
self.peptide_ms1_profiles[peptide][z] = mspy.reduce(
self.peptide_ms1_profiles[peptide][z])
# Summing over each data point
for i, time in enumerate(self.retention_times):
for peptide in self.matched_peptides.keys():
for z in self.matched_peptides[peptide].keys():
if peptide in self.match_data[i].keys() and z in self.match_data[i][peptide].keys():
self.peptide_intensities[peptide][z].append(self.match_data[i][peptide][z].basepeak)
self.peptide_intensities_int[peptide] += self.match_data[i][peptide][z].basepeak
else:
self.peptide_intensities[peptide][z].append(0.0)
def match_peptides_in_scans(
peptides, PatternObjects, ScanList, ms1ScanList, profiles, charge_min, charge_max, mz_min, mz_max, files
):
# Matches expected isotopic distributions of peptides in MS1 spectra
t0 = timer.time()
RetentionTimeData = {}
BasepeakData = {}
RmsdData = {}
ProfileData = {}
IntIntensity = {}
# Iterate through peptide and initiate data structures
for peptide in peptides:
RetentionTimeData[peptide] = {}
BasepeakData[peptide] = {}
RmsdData[peptide] = {}
ProfileData[peptide] = {}
IntIntensity[peptide] = defaultdict(lambda: 1)
# Iterate through charge states and initiate data structures
for z in range(charge_min, charge_max + 1):
RetentionTimeData[peptide][z] = {}
BasepeakData[peptide][z] = {}
RmsdData[peptide][z] = {}
ProfileData[peptide][z] = {}
# Iterate through files and initiate data structures
for file_iter in files:
RetentionTimeData[peptide][z][file_iter] = []
BasepeakData[peptide][z][file_iter] = []
RmsdData[peptide][z][file_iter] = []
ProfileData[peptide][z][file_iter] = None
IntIntensity[peptide][file_iter] += 0
if PatternObjects[peptide][z][0][0] < mz_min or PatternObjects[peptide][z][-1][0] > mz_max:
continue
# Iterate through scans
for scan_number in ms1ScanList[file_iter]:
RetentionTimeData[peptide][z][file_iter].append(ScanList[file_iter][scan_number]["retentionTime"])
checkPatternResult = mspy.checkpattern_fast(
signal=profiles[file_iter][scan_number], pattern=PatternObjects[peptide][z]
)
if checkPatternResult is not None:
RmsdData[peptide][z][file_iter].append(checkPatternResult.rmsd)
BasepeakData[peptide][z][file_iter].append(checkPatternResult.basepeak)
if checkPatternResult.rmsd < RmsdThreshold:
if ProfileData[peptide][z][file_iter] is None:
ProfileData[peptide][z][file_iter] = mspy.crop(
profiles[file_iter][scan_number],
PatternObjects[peptide][z][0][0] - 0.1,
PatternObjects[peptide][z][-1][0] + 0.1,
)
else:
ProfileData[peptide][z][file_iter] = mspy.combine(
ProfileData[peptide][z][file_iter],
mspy.crop(
profiles[file_iter][scan_number],
PatternObjects[peptide][z][0][0] - 0.1,
PatternObjects[peptide][z][-1][0] + 0.1,
),
)
IntIntensity[peptide][file_iter] += checkPatternResult.basepeak
else:
RmsdData[peptide][z][file_iter].append(1)
BasepeakData[peptide][z][file_iter].append(0)
if ProfileData[peptide][z][file_iter] is not None:
ProfileData[peptide][z][file_iter] = mspy.reduce(ProfileData[peptide][z][file_iter])
t1 = timer.time() - t0
print "Loaded files in %s " % t1
MatchData = {}
MatchData["RetentionTime"] = RetentionTimeData
MatchData["Basepeak"] = BasepeakData
MatchData["Rmsd"] = RmsdData
MatchData["Profile"] = ProfileData
MatchData["IntIntensity"] = IntIntensity
return MatchData
