def get_exon (cursor, exon_id, is_known=None, db_name=None): exon = Exon () if (db_name): if not switch_to_db(cursor, db_name): return exon if is_known==2: # sw# exon qry = "select * from sw_exon where exon_id = %d" % exon_id rows = search_db(cursor, qry, verbose=False) if (not rows): return exon exon.load_from_novel_exon (rows[0], "sw_exon") elif is_known==3: # sw# exon qry = "select * from usearch_exon where exon_id = %d" % exon_id rows = search_db(cursor, qry, verbose=False) if (not rows): return exon exon.load_from_novel_exon (rows[0], "usearch_exon") else: qry = "select * from gene2exon where exon_id = %d" % exon_id if is_known: qry += " and is_known = %s " % is_known rows = search_db(cursor, qry, verbose=False) if (not rows): return exon exon.load_from_gene2exon (rows[0]) return exon
def get_exon(cursor, exon_id, is_known=None, db_name=None): exon = Exon() if db_name: if not switch_to_db(cursor, db_name): return exon if is_known == 2: # sw# exon qry = "select * from sw_exon where exon_id = %d" % exon_id rows = search_db(cursor, qry, verbose=False) if not rows: return exon exon.load_from_novel_exon(rows[0], "sw_exon") elif is_known == 3: # sw# exon qry = "select * from usearch_exon where exon_id = %d" % exon_id rows = search_db(cursor, qry, verbose=False) if not rows: return exon exon.load_from_novel_exon(rows[0], "usearch_exon") else: qry = "select * from gene2exon where exon_id = %d" % exon_id if is_known: qry += " and is_known = %s " % is_known rows = search_db(cursor, qry, verbose=False) if not rows: return exon exon.load_from_gene2exon(rows[0]) return exon
def get_novel_exons (cursor, gene_id, table): exons = [] qry = "select * from %s " % table qry += " where gene_id = %d " % int(gene_id) rows = search_db (cursor, qry) if not rows: return exons for row in rows: exon = Exon() exon.load_from_novel_exon (row, table) exons.append(exon) return exons