def gene_from_node_name(self, names):
for name in names:
gene = mygeneinfo.query_standard_to_gene_quick(name)
if gene:
self.term_to_gene_map[name] = gene
self.genes[gene.id] = gene.symbol
return True
else:
print name + " not found in mygene.info"
return False
def gene_symbol_and_id_from_term(self, term):
gene = self.term_to_gene_map.get(term)
if gene:
return gene
else:
# look for term on external service
gene = mygeneinfo.query_standard_to_gene_quick(term)
if gene:
self.term_to_gene_map[term] = gene
return gene
else:
print term + " doesn't map to any gene"
return None
def gene_from_base_term_id(self, base_term_id):
base_term = self.base_term_map.get(base_term_id)
if base_term:
gene = self.term_to_gene_map.get(base_term.name)
if gene:
self.genes[gene.id] = gene
return True
else:
# look for term on external service
gene = mygeneinfo.query_standard_to_gene_quick(base_term.name)
if gene:
self.term_to_gene_map[base_term.name] = gene
self.genes[gene.id] = gene
return True
return False
