def map2exon(cursor, ensembl_db_name, map, paralogue=False):
# this is fake exon info! to be passe to get_exon_pepseq
exon = Exon ()
exon.exon_id = map.exon_id_2
exon.is_known = map.exon_known_2
if map.source == 'sw_sharp':
exon.analysis_id = -1
if not paralogue: # move to the other species
rows = switch_to_db (cursor, ensembl_db_name[map.species_2])
if not rows:
exon.exon_seq_id = -1
return exon
else:
qry = "select exon_seq_id from sw_exon where exon_id = %d " % exon.exon_id
rows = search_db (cursor, qry)
if not rows or not rows[0][0]:
exon.exon_seq_id = -1
else:
exon.exon_seq_id = int(rows[0][0])
elif map.source == 'usearch':
exon.analysis_id = -2
if not paralogue:
rows = switch_to_db (cursor, ensembl_db_name[map.species_2])
if not rows:
exon.exon_seq_id = -1
return exon
else:
qry = "select exon_seq_id from usearch_exon where exon_id = %d " % exon.exon_id
rows = search_db (cursor, qry)
if not rows or not rows[0][0]:
exon.exon_seq_id = -1
else:
exon.exon_seq_id = int(rows[0][0])
else:
exon.analysis_id = 1
return exon
