def __call__(self, seqs):
'It splits a list of sequences with the provided linkers'
stats = self._stats
stats[PROCESSED_PACKETS] += 1
seq_fhand = write_seqrecords(seqs, file_format='fasta')
seq_fhand.flush()
min_identity = 87.0
min_len = 17
filters = [{'kind': 'min_length', 'min_num_residues': min_len,
'length_in_query': False, 'filter_match_parts': True},
{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': min_identity}]
matcher = BlastMatcher(seq_fhand.name, self.linkers,
program='blastn', filters=filters,
params={'task': 'blastn-short'},
elongate_for_global=True)
new_seqs = []
for seqrec in seqs:
stats[PROCESSED_SEQS] += 1
segments = matcher.get_matched_segments_for_read(seqrec.id)
if segments is not None:
split_seqs = self._split_by_mate_linker(seqrec, segments)
else:
split_seqs = [seqrec]
for seq in split_seqs:
new_seqs.append(seq)
stats[YIELDED_SEQS] += 1
return new_seqs
def test_matching_segments(self):
'It tests the detection of oligos in sequence files'
seq_5 = 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC'
mate_fhand = create_a_matepair_file()
expected_region = (len(seq_5), len(seq_5 + TITANIUM_LINKER) - 1)
matcher = BlastMatcher(mate_fhand.name, LINKERS, program='blastn',
elongate_for_global=True)
linker_region = matcher.get_matched_segments_for_read('seq1')[0]
assert [expected_region] == linker_region
def __call__(self, seqrecords):
'It trims the masked segments of the seqrecords.'
stats = self.stats
db_fhand = write_seqrecords(seqrecords, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 89},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
matcher = BlastMatcher(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params, elongate_for_global=True)
for seqrec in seqrecords:
stats[PROCESSED_SEQS] += 1
segments = matcher.get_matched_segments_for_read(seqrec.id)
if segments is not None:
_add_trim_segments(segments[0], seqrec, kind=VECTOR)
stats[YIELDED_SEQS] += 1
return seqrecords
