def get_predicted_exons (cursor, gene_id, species):
exons = []
# get the region on the gene
ret = get_gene_region (cursor, gene_id)
if ret:
[gene_seq_id, gene_region_start, gene_region_end,
gene_region_strand] = ret
else:
print "region not retrived for ", species, gene_id
return []
qry = "SELECT * FROM prediction_exon WHERE seq_region_id = %d " % gene_seq_id
qry += " AND seq_region_start >= %d AND seq_region_start <= %d " % \
(gene_region_start, gene_region_end)
qry += " AND seq_region_end >= %d AND seq_region_end <= %d " % \
(gene_region_start, gene_region_end)
rows = search_db (cursor, qry)
if (not rows):
return []
for row in rows:
exon = Exon()
exon.gene_id = gene_id
exon.load_from_ensembl_prediction (gene_region_start, gene_region_end, row)
exons.append(exon)
return exons
def get_predicted_exons(cursor, gene_id, species):
exons = []
# get the region on the gene
ret = get_gene_region(cursor, gene_id)
if ret:
[gene_seq_id, gene_region_start, gene_region_end, gene_region_strand] = ret
else:
print "region not retrived for ", species, gene_id
return []
qry = "SELECT * FROM prediction_exon WHERE seq_region_id = %d " % gene_seq_id
qry += " AND seq_region_start >= %d AND seq_region_start <= %d " % (gene_region_start, gene_region_end)
qry += " AND seq_region_end >= %d AND seq_region_end <= %d " % (gene_region_start, gene_region_end)
rows = search_db(cursor, qry)
if not rows:
return []
for row in rows:
exon = Exon()
exon.gene_id = gene_id
exon.load_from_ensembl_prediction(gene_region_start, gene_region_end, row)
exons.append(exon)
return exons
def get_known_exons (cursor, gene_id, species):
exons = []
qry = "select distinct exon_transcript.exon_id from exon_transcript, transcript "
qry += " where exon_transcript.transcript_id = transcript.transcript_id "
qry += " and transcript.gene_id = %d " % gene_id
rows = search_db (cursor, qry)
if (not rows ):
return []
if ('Error' in rows[0]):
search_db (cursor, qry, verbose = True)
return []
# get the region on the gene
ret = get_gene_region (cursor, gene_id)
if ret:
[gene_seq_id, gene_region_start, gene_region_end,
gene_region_strand] = ret
else:
print "region not retrived for ", species, gene_id
return []
exon_ids = []
for row in rows:
exon_ids.append(row[0])
for exon_id in exon_ids:
qry = "select * from exon where exon_id=%d" % exon_id
rows = search_db (cursor, qry)
if (not rows or 'Error' in rows[0]):
search_db (cursor, qry, verbose = True)
continue
exon = Exon()
exon.gene_id = gene_id
exon.load_from_ensembl_exon (gene_region_start, gene_region_end, rows[0])
exons.append(exon)
return exons
