def match_decon2ls_isos(spectrum_db, hypothesis, adducts=None, ms1_match_tolerance=1e-5, output_path=None):
if adducts is None:
adducts = [NoShift]
results = RecordDatabase(output_path, record_type=hypothesis.record_type)
results.apply_schema()
for composition in hypothesis:
matches = []
scans_searched = set()
charge_states = set()
for adduct in adducts:
for spectrum in spectrum_db.ppm_match_tolerance_search(
composition.intact_mass + adduct.mass, ms1_match_tolerance):
match_ppm = ppm_error(composition.intact_mass + adduct.mass, spectrum.neutral_mass)
match = PrecursorMatch(
str(composition.id) + ":" + adduct.name, spectrum.neutral_mass, match_ppm,
spectrum.get("abundance"), spectrum.charge, spectrum.other_data,
spectrum.scan_ids[0])
matches.append(match)
scans_searched.update(spectrum.scan_ids)
charge_states.add(spectrum.charge)
groups = groupby(matches, match_key_getter)
composition.precursor_matches = {key: combine_results(group) for key, group in groups.items()}
composition.precursor_scans_searched = scans_searched
composition.precursor_scan_density = density(scans_searched)
composition.precursor_charge_states = charge_states
results.load_data([composition], set_id=False, cast=True, commit=False)
results.commit()
results.apply_indices()
return results
def download_all_structures(db_path, record_type=GlycanRecordWithTaxon): # pragma: no cover
response = requests.get(u'http://www.glycome-db.org/http-services/getStructureDump.action?user=eurocarbdb')
response.raise_for_status()
handle = gzip.GzipFile(fileobj=StringIO(response.content))
xml = etree.parse(handle)
db = RecordDatabase(db_path, record_type=record_type)
misses = []
i = 0
for structure in xml.iterfind(".//structure"):
try:
glycomedb_id = int(structure.attrib['id'])
i += 1
glycoct_str = structure.find("sequence").text
taxa = [Taxon(t.attrib['ncbi'], None, None) for t in structure.iterfind(".//taxon")]
glycan = glycoct.loads(glycoct_str)
if (glycoct.loads(str(glycan)).mass() - glycan.mass()) > 0.00001:
raise Exception("Mass did not match on reparse")
record = record_type(glycan, taxa=taxa, id=glycomedb_id)
db.load_data(record, commit=False, set_id=False)
if i % 1000 == 0:
print(i, "Records parsed.")
except Exception as e:
misses.append((glycomedb_id, e))
print(glycomedb_id, e)
db.set_metadata("misses", misses)
db.commit()
return db
