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 gene2exon_list(cursor, gene_id, db_name=None, verbose=False):
exons = []
if db_name:
if not switch_to_db(cursor, db_name):
return False
qry = "select * from gene2exon where gene_id = %d " % gene_id
rows = search_db(cursor, qry)
if not rows:
rows = search_db(cursor, "select database()")
if verbose:
print "database ", rows[0][0]
rows = search_db(cursor, qry, verbose=True)
print rows
return []
for row in rows:
exon = Exon()
if not exon.load_from_gene2exon(row):
continue
exons.append(exon)
return exons
def gene2exon_list (cursor, gene_id, db_name=None, verbose=False):
exons = []
if (db_name):
if not switch_to_db(cursor, db_name):
return False
qry = "select * from gene2exon where gene_id = %d " % gene_id
rows = search_db(cursor, qry)
if (not rows):
rows = search_db(cursor, 'select database()')
if verbose:
print "database ", rows[0][0]
rows = search_db(cursor, qry, verbose = True)
print rows
return []
for row in rows:
exon = Exon()
if (not exon.load_from_gene2exon(row)):
continue
exons.append(exon)
return exons