def _parse_massbank_file(self, f_path):
print "Parse file:", f_path
# read ms/ms file in
f = open(f_path)
data = f.read()
f.close()
# create Spectrum instance
spectrum = Spectrum(f_path)
# set f_name
spectrum.f_name = f_path
# set precursor
_precursor = re.findall(
"MS\$FOCUSED_ION: PRECURSOR_M/Z[: ]+([0-9\.]+)", data)
if len(_precursor) > 0:
precursor = float(_precursor[0])
else:
_basepeak = re.findall("MS\$FOCUSED_ION: BASE_PEAK[: ]+([0-9\.]+)",
data)
if len(_basepeak) > 0:
print("WARNING: using base peak as precursor for %s!" % f_path)
precursor = float(_basepeak[0])
else:
raise Exception("ERROR: precursor not set for %s!" % f_path)
spectrum.precursor = precursor
# set ion mode
_mode = re.findall("ION_MODE ([A-Z]+)", data)
if len(_mode) > 0:
mode = _mode[0]
else:
_mode = re.findall("MODE ([A-Z]+)", data)
if len(_mode) > 0:
print("WARNING: ion mode is set by MODE for %s!" % f_path)
mode = _mode[0]
else:
raise Exception("ERROR: mode not set for %s!" % f_path)
spectrum.mode = mode
if spectrum.mode == 'POSITIVE':
spectrum.mass = spectrum.precursor - 1.00794
else:
spectrum.mass = spectrum.precursor + 1.00794
_ppm = re.findall("SE\$SEARCH_PPM[: ]+([0-9\.]+)", data)
if len(_ppm) > 0:
ppm = int(_ppm[0])
else:
raise Exception("ERROR: PPM not set for %s!" % f_path)
spectrum.ppm = ppm
# set peaks
_peaks = []
lines = data.split("\n")
ready = False
for line in lines:
if len(line) == 0:
continue
if line.find("PK$PEAK") != -1:
ready = True
continue
if ready:
if line.find("N/A") != -1:
raise Exception("ERROR: no peaks in %s" % f_path)
words = line.split()
mass = float(words[0])
inten = float(words[1])
#mass = mass+numpy.random.normal(0,1e-8,1) # add noise
#mass = float("%.3f" % mass)
_peaks.append((mass, inten))
spectrum.peaks = _peaks
_ce = re.findall("COLLISION_ENERGY (\w+)", data)
if len(_ce) > 0:
ce = _ce[0]
ce = ce.replace("eV", "")
if ce.isdigit():
spectrum.ce = int(ce)
return spectrum
def _parse_massbank_file(self, f_path):
print "Parse file:",f_path
# read ms/ms file in
f = open(f_path)
data = f.read()
f.close()
# create Spectrum instance
spectrum = Spectrum(f_path)
# set f_name
spectrum.f_name = f_path
# set precursor
_precursor = re.findall("MS\$FOCUSED_ION: PRECURSOR_M/Z[: ]+([0-9\.]+)",data)
if len(_precursor) > 0:
precursor = float(_precursor[0])
else:
_basepeak = re.findall("MS\$FOCUSED_ION: BASE_PEAK[: ]+([0-9\.]+)",data)
if len(_basepeak)>0 :
print ("WARNING: using base peak as precursor for %s!" % f_path)
precursor = float(_basepeak[0])
else:
raise Exception("ERROR: precursor not set for %s!" % f_path)
spectrum.precursor = precursor
# set ion mode
_mode = re.findall("ION_MODE ([A-Z]+)", data)
if len(_mode) > 0:
mode = _mode[0]
else:
_mode = re.findall("MODE ([A-Z]+)", data)
if len(_mode)>0:
print ("WARNING: ion mode is set by MODE for %s!" % f_path)
mode = _mode[0]
else:
raise Exception("ERROR: mode not set for %s!" % f_path)
spectrum.mode = mode
if spectrum.mode == 'POSITIVE':
spectrum.mass = spectrum.precursor - 1.00794
else:
spectrum.mass = spectrum.precursor + 1.00794
_ppm = re.findall("SE\$SEARCH_PPM[: ]+([0-9\.]+)",data)
if len(_ppm) > 0:
ppm = int(_ppm[0])
else:
raise Exception("ERROR: PPM not set for %s!" % f_path)
spectrum.ppm = ppm
# set peaks
_peaks = []
lines = data.split("\n"); ready = False
for line in lines:
if len(line) == 0:
continue
if line.find("PK$PEAK") != -1:
ready = True
continue
if ready:
if line.find("N/A") != -1:
raise Exception("ERROR: no peaks in %s" % f_path)
words = line.split()
mass = float(words[0])
inten = float(words[1])
#mass = mass+numpy.random.normal(0,1e-8,1) # add noise
#mass = float("%.3f" % mass)
_peaks.append((mass,inten))
spectrum.peaks = _peaks
_ce = re.findall("COLLISION_ENERGY (\w+)",data)
if len(_ce) > 0:
ce = _ce[0]
ce = ce.replace("eV","")
if ce.isdigit():
spectrum.ce = int(ce)
return spectrum
