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