def get_homologs_for_gene(self, symbol, org_name):
# always use FlyMine for querying homologs
service = self.services["Drosophila melanogaster"]
query = service.new_query()
query.add_view(
"Gene.symbol", "Gene.primaryIdentifier", "Gene.homologues.homologue.symbol",
"Gene.homologues.homologue.primaryIdentifier",
"Gene.homologues.homologue.organism.name",
"Gene.homologues.dataSets.name"
)
query.add_constraint("Gene.homologues.homologue.organism.name", "ONE OF", org_util.get_names())
query.add_constraint("Gene.organism.name", "=", org_name)
query.add_constraint("Gene.symbol", "=", symbol)
homologs = defaultdict(lambda: defaultdict(list))
for row in query.results("tsv"):
cols = row.split('\t')
homolog_org = cols[4]
homolog_symbol = cols[2]
if homolog_symbol != '""':
if len(cols) == 6:
dataset = self.strip_suffix(cols[5])
homologs[homolog_org][homolog_symbol].append(dataset)
else:
homologs[homolog_org][homolog_symbol].append(None)
return homologs
def get_homologs_for_gene(self, symbol, org_name):
# always use FlyMine for querying homologs
h_sym = "homologues.homologue.symbol"
h_org = "homologues.homologue.organism.name"
h_ds = "homologues.dataSets.name"
service = self.services["Drosophila melanogaster"]
query = service.new_query("Gene")\
.select(h_org, h_sym, h_ds)\
.where(h_org, "ONE OF", org_util.get_names())\
.where("organism.name", "=", org_name)\
.where("symbol", "=", symbol)\
.where(h_sym, "IS NOT NULL")
homologs = defaultdict(dict)
for org, g1 in groupby(query.rows(), lambda x: x[h_org]):
for sym, g2 in groupby(g1, lambda x: x[h_sym]):
homologs[org][sym] = [r[h_ds] for r in g2]
return homologs
