def test_multi_processing_blast(self):
""" Test that a set of blast runs using multiprocessing run """
fn_database = os.path.join(self.datadir, "mini_nr", "nr_test2")
blaster = BLASTUtilities.BLASTMultiProcessing()
parser = SeqIO.parse(fn_database, "fasta")
identifier = "temp.{0}"
i = 0
n_seqs = 20
for seq_record in parser:
if i == n_seqs:
break
blaster.add_sequence(seq_record.seq.tostring(),
identifier.format(i), fn_database)
i += 1
fn_identifier_pairs = blaster.run()
self.assertEqual(len(fn_identifier_pairs), n_seqs,
"Unexpected number of BLAST results")
blast_parser = BLASTUtilities.BLASTMultiProcessingParser()
for i, fn in fn_identifier_pairs:
blast_parser.add_file(identifier.format(i), fn)
parsing_results = blast_parser.run()
l = len(parsing_results)
self.assertEqual(l, n_seqs,
"Unexpected number of parsed results {0}".format(l))
for i, fn in fn_identifier_pairs:
os.remove(fn)
def blast(seqs):
"""
Blast a set of sequences and parse the results. The function does calls the
MultiProcessing versions
@seqs A list of tuples of (sequence, identifier for the sequence, database to use
for the blast procedure)
@return Returns a list of BLASTResult objects
"""
if len(seqs) == 0:
raise ValueError("No sequences provided")
blaster = BLASTUtilities.BLASTMultiProcessing()
log.debug("Running blast from %s sequences",len(seqs))
for seq in seqs:
blaster.add_sequence(*seq)
fns_blast_output = blaster.run()
parser = BLASTUtilities.BLASTMultiProcessingParser()
for identifier, fn in fns_blast_output:
parser.add_file(identifier, fn)
parsing_results = parser.run()
# clean xmls after parsing
for i,fn in fns_blast_output:
os.remove(fn)
return parsing_results
