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 blast_record_set(dbfile_path, fasta_records, blast_prefs):
"""Loop through fasta entries and blast against database."""
import os
from analysis.seqfile_ops import write_fasta
from analysis.blasting import local_blastn
matches = {}
for query_record in fasta_records:
query_file = 'temp.fas'
out_file = 'temp.blast'
write_fasta(query_file,query_record)
try:
status = local_blastn(query_file, out_file, dbfile_path,
blast_prefs)
except: raise
else:
query_matches = parse_blast_out6(out_file, blast_prefs)
matches[query_record.id] = query_matches
finally:
os.remove(query_file)
os.remove(out_file)
return matches
