def _parse(self, line: str):
items = [i.strip() for i in line.split('\t')]
assert len(items) > 1, line
for idx in range(len(items)):
if items[idx] == '-':
items[idx] = ''
while len(items) < 16:
items.append('')
row = Line._make(items)
record = GeneRecord(Species.human, symbol=row.symbol, name=row.name,
location=row.location if row.location else None)
db_key = DBRef(Namespace.hgnc, row.id)
record.addDBRef(db_key)
# link DB references
for ns in DB_REFS:
acc = getattr(row, ns)
if acc:
if ns in FIX_ACCESSION:
# noinspection PyUnresolvedReferences
acc = acc[acc.find(":") + 1:]
ref = DBRef(ns, acc)
if ref in WRONG_DB_REFS:
new_ref = WRONG_DB_REFS[ref]
logging.info('correcting wrong ref %s->%s',
'{}:{}'.format(*ref),
'{}:{}'.format(*new_ref))
ref = new_ref
record.addDBRef(ref)
# parse symbol strings
for field in (row.previous_symbols, row.synonyms):
if field:
for symbol in Parser._parseCD(field):
record.addSymbol(symbol)
# parse name strings
for field in (row.previous_names, row.name_synonyms):
if field:
for name in Parser._parseQCD(field):
record.addName(name)
# parse keywords strings
if row.gene_family_symbols:
for kwd in Parser._parseCD(row.gene_family_symbols):
record.addKeyword(kwd)
# location with ALT_REF_LOCI values - eliminate them
if row.location and " ALT_REF_LOCI" in row.location:
record.location = row.location[:row.location.find(" ALT_REF_LOCI")]
for name in Parser._parseQCD(row.gene_family_names):
for subname in name.split(' / '):
for subsubname in subname.split(' : '):
subsubname = subsubname.strip()
if subsubname.lower() not in ('other', '"other"'):
record.addKeyword(subsubname)
try:
self._loadRecord(db_key, record)
except DuplicateEntityError:
if len(record.refs) == 2:
# assume all HGNC links that do not coincide with the
# Entrez back-link are bad, as it seems it is mostly
# HGNC that is not up-to-date.
logging.warn('removing likely bad Entrez ref in %s:%s',
*db_key)
assert any(r.namespace == Namespace.entrez
for r in record.refs), record.refs
record.refs = {r for r in record.refs if
r.namespace == Namespace.hgnc}
assert len(record.refs) == 1, record.refs
self._loadRecord(db_key, record)
else:
raise
return 1
