def test_blast_record_set(self):
# prepare database
seqfile_ops.write_fasta(self.db_file, self.db_records)
db_records_list = seqfile_ops.load_multifasta(self.db_file)
index = 0
for record in db_records_list:
self.assertEqual(record.id,self.db_records[index].id)
self.assertEqual(str(record.seq),str(self.db_records[index].seq))
index +=1
# make database
self.dbfile_path, db_report = blasting.make_blastDB(self.temp_dir,
self.db_name,
self.db_file,
'nucl')
self.assertIs(db_report['status'], 0)
self.assertEquals(db_report['message'], 'database exists')
# run local blast batch (with multiple queries)
matches_multi = blasting.blast_record_set(self.dbfile_path,
self.multi_records,
self.prefs)
self.assertIs(len(matches_multi), 3)
index = 0
for record in self.multi_records:
self.assertEqual(matches_multi[record.id][0]['contig_id'],
self.multi_records[index].id)
self.assertEqual(matches_multi[record
.id][0]['details']['match_p100'], 100)
index +=1
def run_blast(self, blast_run):
query_segs = blast_run.query.query_segs
blast_prefs = blast_run.parameters
matches_dict = blast_record_set(self.name, query_segs, blast_prefs)
self.match_sets.append({"run_id": blast_run.run_id, "matches": matches_dict})