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
