def test_local_blastn(self):
# prepare query
seqfile_ops.write_fasta(self.single_q_file, self.single_record)
query_record = seqfile_ops.load_fasta(self.single_q_file)
self.assertEqual(query_record.id,self.record_1.id)
self.assertEqual(str(query_record.seq),str(self.record_1.seq))
# prepare database
seqfile_ops.write_fasta(self.db_file, self.db_records)
records_list = seqfile_ops.load_multifasta(self.db_file)
index = 0
for record in 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 with single query
self.status = blasting.local_blastn(self.single_q_file,
self.single_out_file,
self.dbfile_path,
self.prefs)
self.assertEquals(self.status['output'], '')
self.assertIsNone(self.status['error'])
# parse blast output
matches_single = blasting.parse_blast_out6(self.single_out_file,
self.prefs)
self.assertIs(len(matches_single), 1)
self.assertEqual(matches_single[0]['contig_id'],
self.single_record.id)
self.assertEqual(matches_single[0]['details']['match_p100'], 100)
def test_write_and_load_single_fasta(self):
count = seqfile_ops.write_fasta(self.fas_filename, self.record)
self.assertIs(count, 1)
fas_record = seqfile_ops.load_fasta(self.fas_filename)
self.assertEqual(fas_record.id, self.record.id)
