def _setup_checks(self, filterpacket):
seqs = [s for seqs in filterpacket[SEQS_PASSED] for s in seqs]
self._matcher = Blaster(seqs,
self._blast_db,
dbtype=self._dbtype,
program=self._blast_program,
filters=self._filters)
def xtest_blaster(self):
seq = 'GAGAAATTCCTTTGGAAGTTATTCCGTAGCATAAGAGCTGAAACTTCAGAGCAAGTTT'
seq += 'TCATTGGGCAAAATGGGGGAACAACCTATCTTCAGCACTCGAGCTCATGTCTTCCAAATTGA'
seq += 'CCCAAACACAAAGAAGAACTGGGTACCCACCAGCAAGCATGCAGTTACTGTGTCTTATTTCT'
seq += 'ATGACAGCACAAGAAATGTGTATAGGATAATCAGTTTAGATGGCTCAAAGGCAATAATAAAT'
seq += 'AGTACCATCACCCCAAACATGACA'
seqrec = SeqWrapper(SEQRECORD, SeqRecord(Seq(seq), id='seq'), None)
blaster = Blaster([seqrec], 'nr', 'blastn', remote=True)
print blaster.get_matched_segments('seq')
assert blaster.get_matched_segments('seq') == [(1, 1740)]
def __call__(self, seqrecords):
'It does the work'
if not seqrecords:
return seqrecords
matcher = Blaster(seqrecords,
self.blastdb,
self._program,
self._dbtype,
filters=self._filters,
params=self._params,
remote=self._remote)
blasts = matcher.blasts
blastdb = os.path.basename(self.blastdb)
for seqrecord in seqrecords:
align_result = blasts.get(get_name(seqrecord), None)
if not align_result:
continue
match_counter = 0
for match in align_result['matches']:
subject = match['subject']['name']
match_counter += 1
for match_part in match['match_parts']:
if match_part['subject_end'] < match_part['subject_start']:
strand = -1
subject_start = match_part['subject_end']
subject_end = match_part['subject_start']
else:
strand = 1
subject_start = match_part['subject_start']
subject_end = match_part['subject_end']
query_start = match_part['query_start']
query_end = match_part['query_end']
qualifiers = {}
qualifiers['Target'] = {
'start': subject_start,
'end': subject_end,
'name': subject
}
qualifiers['score'] = match_part['scores']['expect']
qualifiers['identity'] = match_part['scores']['identity']
qualifiers['blastdb'] = blastdb
location = FeatureLocation(query_start, query_end, strand)
feature = SeqFeature(
location=location,
type='match_part',
qualifiers=qualifiers,
id='match{0:03d}'.format(match_counter))
seqrecord.object.features.append(feature)
return seqrecords
