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 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)]
class FilterBlastMatch(_BaseFilter):
'It filters a seq if there is a match against a blastdb'
def __init__(self, database, program, filters, dbtype=None,
failed_drags_pair=True, reverse=False):
'''The initiator
database: path to a file with seqs or a blast database
filter_params:
expect_threshold
similarty treshlod
min_length_percentaje
'''
self._blast_db = database
self._blast_program = program
self._filters = filters
self._dbtype = dbtype
super(FilterBlastMatch, self).__init__(reverse=reverse,
failed_drags_pair=failed_drags_pair)
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 _do_check(self, seq):
segments = self._matcher.get_matched_segments(get_name(seq))
return True if segments is None else False
class FilterBlastMatch(_BaseFilter):
'It filters a seq if there is a match against a blastdb'
def __init__(self, database, program, filters, dbtype=None,
failed_drags_pair=True, reverse=False):
'''The initiator
database: path to a file with seqs or a blast database
filter_params:
expect_threshold
similarty treshlod
min_length_percentaje
'''
self._blast_db = database
self._blast_program = program
self._filters = filters
self._dbtype = dbtype
super(FilterBlastMatch, self).__init__(reverse=reverse,
failed_drags_pair=failed_drags_pair)
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 _do_check(self, seq):
segments = self._matcher.get_matched_segments(get_name(seq))
return True if segments is None else False
