def _parse_metlin_file(self, f_path, kegg_mass, inchi):
tree = ET.parse(f_path)
root = tree.getroot()
eles = root.findall("./ExperimentInformations/Comment")
for ele in eles:
if ele.get('Id')=='kegg':
kegg_id = ele.get('Value')
if ele.get('Id') == 'Metlin-ID':
metlin_id = ele.get('Value')
if ele.get("Id") == 'cas':
cas = ele.get('Value')
eles = root.findall("./ExperimentInformations")
for ele in eles: # should have only one element
mass_diff = float(ele.attrib['ModificationMass'])
c_name = ele.attrib['CompoundName']
c_formula = ele.attrib['MolecularFormula']
spectra = []; spectra_ms1 = []
eles = root.findall("./Spectra/Spectrum")
for ele in eles:
if ele.get("MSLevel") == "1":
spectra_ms1.append(ele)
if ele.get("MSLevel") == "2":
spectra.append(ele)
if kegg_id not in kegg_mass:
print "Ignore %s:kegg_mass doesn't have %s" % (f_path,kegg_id)
return []
if kegg_id not in inchi:
print "Ignore %s:kegg_inchi doesn't have %s" % (f_path,kegg_id)
return []
mass = kegg_mass[kegg_id]
inchi = inchi[kegg_id]
spectra_list = []
for spec in spectra:
ce = int(spec.attrib['CollisionEnergy'])
spectrum = Spectrum()
spectrum.f_name = f_path
spectrum.mass = float(mass)
spectrum.precursor = mass + mass_diff
spectrum.mode = "POSITIVE"
spectrum.inchi = inchi
spectrum.cas = cas
spectrum.pubchem_sid = "NULL"
spectrum.pubchem_cid = "NULL"
spectrum.kegg_id = kegg_id
spectrum.metlin_id = metlin_id
spectrum.ce = ce
peaks = spec.findall("Peak")
_peaks = []
for peak in peaks:
_mass = float(peak.get("Mass")); _inten = float(peak.get("Intensity"))
if _inten > 1:
_peaks.append((_mass,_inten/100))
spectrum.peaks = _peaks
spectra_list.append(spectrum)
return spectra_list
def _parse_ms_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 metlin id
spectrum.metlin_id = f_path[f_path.find("pos") + 3:f_path.find(".")]
# set precursor
_precursor = re.findall("parentmass[: ]+([0-9\.]+)", data)
if len(_precursor) > 0:
precursor = float(_precursor[0])
else:
raise Exception("ERROR: precursor not set for %s!" % f_path)
spectrum.precursor = precursor
spectrum.mass = precursor - 1.00794
# set peaks and intensity
_peaks = []
seg = False
for line in data.split('\n'):
if line.find("collision") != -1:
seg = True
continue
if not line:
seg = False
continue
if seg:
words = line.split()
mass = float(words[0])
inten = float(words[1])
_peaks.append((mass, inten))
spectrum.peaks = _peaks
return spectrum
def _parse_ms_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 metlin id
spectrum.metlin_id = f_path[f_path.find("pos")+3:f_path.find(".")]
# set precursor
_precursor = re.findall("parentmass[: ]+([0-9\.]+)",data)
if len(_precursor) > 0:
precursor = float(_precursor[0])
else:
raise Exception("ERROR: precursor not set for %s!" % f_path)
spectrum.precursor = precursor
spectrum.mass = precursor - 1.00794
# set peaks and intensity
_peaks = []
seg = False
for line in data.split('\n'):
if line.find("collision") != -1:
seg = True
continue
if not line:
seg = False
continue
if seg:
words = line.split()
mass = float(words[0])
inten = float(words[1])
_peaks.append((mass,inten))
spectrum.peaks = _peaks
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 mass
_mass = re.findall("CH\$EXACT_MASS[: ]+([0-9\.]+)", data)
if len(_mass) > 0:
mass = float(_mass[0])
else:
raise Exception("ERROR: mass filed error in file %s " % f_path)
spectrum.mass = mass
# 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
# 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
# set inchi
_inchi = re.findall("IUPAC: (.+)",data)
if len(_inchi) > 0:
if _inchi[0].find('unknown') != -1:
print f_path, 'has no inchi!'
inchi = _inchi[0]
#raise Exception("Error: no inchi for %s!" % f_path)
else:
inchi = _inchi[0]
else:
raise Exception("Error: no inchi for %s!" % f_path)
if "InChI=" not in inchi: # some inchi may not contains the head
inchi = "InChI=" + inchi
spectrum.inchi = inchi
# below are optional field for Spectrum
_cas = re.findall("CH\$LINK: CAS[: ]+([0-9\-]+)", data)
if len(_cas) > 0:
cas = _cas[0]
spectrum.cas = cas
_metlin = re.findall("CH\$LINK: METLIN[: ]+([0-9]+)", data)
if len(_metlin) > 0:
metlin = _metlin[0]
spectrum.metlin_id = metlin
else:
spectrum.metlin_id = 'NULL'
_sid = re.findall("PUBCHEM SID[: ]+(\w+)", data)
if len(_sid) > 0:
sid = _sid[0]
spectrum.pubchem_sid = sid
else:
_sid = re.findall("PUBCHEM[: ]+([0-9]+)", data)
if len(_sid) > 0:
sid = _sid[0]
spectrum.pubchem_sid = sid
_cid = re.findall("PUBCHEM CID[: ]+(\w+)", data)
if len(_cid) > 0:
cid = _cid[0]
spectrum.pubchem_cid = cid
_kegg_id = re.findall("LINK: KEGG (\w+)", data)
if len(_kegg_id) > 0:
kegg_id = _kegg_id[0]
spectrum.kegg_id = kegg_id
_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_metlin_file(self, f_path, kegg_mass, inchi):
tree = ET.parse(f_path)
root = tree.getroot()
eles = root.findall("./ExperimentInformations/Comment")
for ele in eles:
if ele.get('Id') == 'kegg':
kegg_id = ele.get('Value')
if ele.get('Id') == 'Metlin-ID':
metlin_id = ele.get('Value')
if ele.get("Id") == 'cas':
cas = ele.get('Value')
eles = root.findall("./ExperimentInformations")
for ele in eles: # should have only one element
mass_diff = float(ele.attrib['ModificationMass'])
c_name = ele.attrib['CompoundName']
c_formula = ele.attrib['MolecularFormula']
spectra = []
spectra_ms1 = []
eles = root.findall("./Spectra/Spectrum")
for ele in eles:
if ele.get("MSLevel") == "1":
spectra_ms1.append(ele)
if ele.get("MSLevel") == "2":
spectra.append(ele)
if kegg_id not in kegg_mass:
print "Ignore %s:kegg_mass doesn't have %s" % (f_path, kegg_id)
return []
if kegg_id not in inchi:
print "Ignore %s:kegg_inchi doesn't have %s" % (f_path, kegg_id)
return []
mass = kegg_mass[kegg_id]
inchi = inchi[kegg_id]
spectra_list = []
for spec in spectra:
ce = int(spec.attrib['CollisionEnergy'])
spectrum = Spectrum()
spectrum.f_name = f_path
spectrum.mass = float(mass)
spectrum.precursor = mass + mass_diff
spectrum.mode = "POSITIVE"
spectrum.inchi = inchi
spectrum.cas = cas
spectrum.pubchem_sid = "NULL"
spectrum.pubchem_cid = "NULL"
spectrum.kegg_id = kegg_id
spectrum.metlin_id = metlin_id
spectrum.ce = ce
peaks = spec.findall("Peak")
_peaks = []
for peak in peaks:
_mass = float(peak.get("Mass"))
_inten = float(peak.get("Intensity"))
if _inten > 1:
_peaks.append((_mass, _inten / 100))
spectrum.peaks = _peaks
spectra_list.append(spectrum)
return spectra_list