def getGeneByStableId(self, StableId):
"""returns the gene matching StableId, or None if no record found"""
query = self._get_gene_query(self.CoreDb, StableId=StableId)
try:
record = list(query.execute())[0]
gene = Gene(self, self.CoreDb, data=record)
except IndexError:
gene = None
return gene
def getGenesMatching(self,
Symbol=None,
Description=None,
StableId=None,
BioType=None,
like=True):
"""Symbol: HGC gene symbol, case doesn't matter
description: a functional description
StableId: the ensebl identifier
BioType: the biological encoding type"""
# TODO additional arguments to satisfy: external_ref, go_terms
if Symbol is not None:
Symbol = Symbol.lower()
# biotype -> gene
# description -> gene
# Symbols -> xref
# StableId -> gene_stable_id
# XREF table calls
# for gene symbols, these need to be matched against the display_label
# attribute of core.xref table
# for description, these need to be matched against the description
# field of the xref table
# TODO catch conditions where user passes in both a symbol and a
# biotype
args = dict(Symbol=Symbol,
Description=Description,
StableId=StableId,
BioType=BioType,
like=like)
query = self._get_gene_query(self.CoreDb, **args)
records = query.execute()
if records.rowcount == 0 and Symbol is not None:
# see if the symbol has a synonym
Symbol = self._get_symbol_from_synonym(self.CoreDb, Symbol)
if Symbol is not None:
args['Symbol'] = Symbol
records = self._get_gene_query(self.CoreDb, **args).execute()
else:
records = []
for record in records:
gene = Gene(self, self.CoreDb, data=record)
yield gene