def __call__(self, seqs):
'It splits a list of sequences with the provided linkers'
seq_fhand = write_seqs(seqs, file_format='fasta')
seq_fhand.flush()
min_identity = 87.0
min_len = 13
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 = BlasterForFewSubjects(seq_fhand.name, self.linkers,
program='blastn', filters=filters,
params={'task': 'blastn-short'},
elongate_for_global=True,
seqs_type=NUCL)
new_seqs = []
for seq in seqs:
segments = matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
split_seqs = self._split_by_mate_linker(seq, segments)
else:
split_seqs = [seq]
for seq in split_seqs:
new_seqs.append(seq)
return new_seqs
def __call__(self, seqs):
'It splits a list of sequences with the provided linkers'
seq_fhand = write_seqs(seqs, file_format='fasta')
seq_fhand.flush()
min_identity = 87.0
min_len = 13
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 = BlasterForFewSubjects(seq_fhand.name,
self.linkers,
program='blastn',
filters=filters,
params={'task': 'blastn-short'},
elongate_for_global=True,
seqs_type=NUCL)
new_seqs = []
for seq in seqs:
segments = matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
split_seqs = self._split_by_mate_linker(seq, segments)
else:
split_seqs = [seq]
for seq in split_seqs:
new_seqs.append(seq)
return new_seqs
def _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED]for s in seqs]
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 87},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=True)
def test_matching_segments(self):
'It tests the detection of oligos in sequence files'
seq_5 = 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC'
mate_fhand = create_a_matepair_file()
linkers = assing_kind_to_seqs(SEQRECORD, LINKERS, None)
expected_region = (len(seq_5), len(seq_5 + TITANIUM_LINKER) - 1)
matcher = BlasterForFewSubjects(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 test_matching_segments(self):
'It tests the detection of oligos in sequence files'
seq_5 = 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC'
mate_fhand = create_a_matepair_file()
linkers = [SeqItem('titan', ['>titan\n', TITANIUM_LINKER + '\n']),
SeqItem('flx', ['>flx\n', FLX_LINKER + '\n'])]
linkers = assing_kind_to_seqs(SEQITEM, linkers, 'fasta')
expected_region = (len(seq_5), len(seq_5 + TITANIUM_LINKER) - 1)
matcher = BlasterForFewSubjects(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
class TrimWithBlastShort(_BaseTrim):
'It trims adaptors with the blast short algorithm'
def __init__(self, oligos):
'The initiator'
self.oligos = oligos
super(TrimWithBlastShort, self).__init__()
def _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED] for s in seqs]
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{
'kind': 'score_threshold',
'score_key': 'identity',
'min_score': 87
}, {
'kind': 'min_length',
'min_num_residues': 13,
'length_in_query': False
}]
self._matcher = BlasterForFewSubjects(db_fhand.name,
self.oligos,
program='blastn',
filters=filters,
params=params,
elongate_for_global=True)
def _do_trim(self, seq):
'It trims the masked segments of the SeqWrappers.'
segments = self._matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
_add_trim_segments(segments[0], seq, kind=VECTOR)
return seq
class FilterBlastShort(_BaseFilter):
'It filters a seq if there is a match against the given oligos'
def __init__(self, oligos, failed_drags_pair=True, reverse=False):
self.oligos = oligos
super(FilterBlastShort, 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]
# we create a blastdb for these reads and then we use the oligos
# as the blast query
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 87},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=False)
def _do_check(self, seq):
segments = self._matcher.get_matched_segments_for_read(get_name(seq))
return True if segments is None else False
class TrimWithBlastShort(_BaseTrim):
"It trims adaptors with the blast short algorithm"
def __init__(self, oligos):
"The initiator"
self.oligos = oligos
super(TrimWithBlastShort, self).__init__()
def _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED] for s in seqs]
db_fhand = write_seqs(seqs, file_format="fasta")
db_fhand.flush()
params = {"task": "blastn-short", "expect": "0.0001"}
filters = [
{"kind": "score_threshold", "score_key": "identity", "min_score": 87},
{"kind": "min_length", "min_num_residues": 13, "length_in_query": False},
]
self._matcher = BlasterForFewSubjects(
db_fhand.name, self.oligos, program="blastn", filters=filters, params=params, elongate_for_global=True
)
def _do_trim(self, seq):
"It trims the masked segments of the SeqWrappers."
segments = self._matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
_add_trim_segments(segments[0], seq, kind=VECTOR)
return seq
class FilterBlastShort(_BaseFilter):
'It filters a seq if there is a match against the given oligos'
def __init__(self, oligos, failed_drags_pair=True, reverse=False):
self.oligos = oligos
super(FilterBlastShort, 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]
# we create a blastdb for these reads and then we use the oligos
# as the blast query
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 87},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=False)
def _do_check(self, seq):
segments = self._matcher.get_matched_segments_for_read(get_name(seq))
return True if segments is None else False
class TrimWithBlastShort(_BaseTrim):
'It trims adaptors with the blast short algorithm'
def __init__(self, oligos):
'The initiator'
self.oligos = oligos
super(TrimWithBlastShort, self).__init__()
def _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED]for s in seqs]
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 87},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=True)
def _do_trim(self, seq):
'It trims the masked segments of the SeqWrappers.'
segments = self._matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
_add_trim_segments(segments[0], seq, kind=VECTOR)
return seq
def _setup_checks(self, filterpacket):
seqs = [s for seqs in filterpacket[SEQS_PASSED]for s in seqs]
# we create a blastdb for these reads and then we use the oligos
# as the blast query
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 87},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=False)
class TrimNexteraAdapters(_BaseTrim):
"It trims from Nextera adaptors found with blast short algorithm to 3'end"
"If adapter is at one end and it is not complete, it trims more bases"
def __init__(self, oligos):
'The initiator'
self.oligos = oligos
super(TrimNexteraAdapters, self).__init__()
def _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED]for s in seqs]
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 87},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=True)
def _do_trim(self, seq):
'It trims the masked segments of the SeqWrappers.'
segments = self._matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
segments = [(segment[0], get_length(seq) - 1) for segment in segments[0]]
_add_trim_segments(segments, seq, kind=OTHER)
return seq
def __call__(self, seqs):
'It trims the masked segments of the SeqWrappers.'
db_fhand = write_seqs(seqs, 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 = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=True)
for seq in seqs:
segments = matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
_add_trim_segments(segments[0], seq, kind=VECTOR)
return seqs
def test_matching_segments(self):
'It tests the detection of oligos in sequence files'
seq_5 = 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC'
mate_fhand = create_a_matepair_file()
linkers = [
SeqItem('titan', ['>titan\n', TITANIUM_LINKER + '\n']),
SeqItem('flx', ['>flx\n', FLX_LINKER + '\n'])
]
linkers = assing_kind_to_seqs(SEQITEM, linkers, 'fasta')
expected_region = (len(seq_5), len(seq_5 + TITANIUM_LINKER) - 1)
matcher = BlasterForFewSubjects(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 _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED] for s in seqs]
db_fhand = write_seqs(seqs, file_format="fasta")
db_fhand.flush()
params = {"task": "blastn-short", "expect": "0.0001"}
filters = [
{"kind": "score_threshold", "score_key": "identity", "min_score": 87},
{"kind": "min_length", "min_num_residues": 13, "length_in_query": False},
]
self._matcher = BlasterForFewSubjects(
db_fhand.name, self.oligos, program="blastn", filters=filters, params=params, elongate_for_global=True
)
def _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED]for s in seqs]
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 87},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=True)
def _setup_checks(self, filterpacket):
seqs = [s for seqs in filterpacket[SEQS_PASSED]for s in seqs]
# we create a blastdb for these reads and then we use the oligos
# as the blast query
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 87},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=False)
class TrimNexteraAdapters(_BaseTrim):
"It trims from Nextera adaptors found with blast short algorithm to 3'end"
"If adapter is at one end and it is not complete, it trims more bases"
def __init__(self, oligos):
'The initiator'
self.oligos = oligos
super(TrimNexteraAdapters, self).__init__()
def _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED] for s in seqs]
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{
'kind': 'score_threshold',
'score_key': 'identity',
'min_score': 87
}, {
'kind': 'min_length',
'min_num_residues': 13,
'length_in_query': False
}]
self._matcher = BlasterForFewSubjects(db_fhand.name,
self.oligos,
program='blastn',
filters=filters,
params=params,
elongate_for_global=True)
def _do_trim(self, seq):
'It trims the masked segments of the SeqWrappers.'
segments = self._matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
segments = [(segment[0], get_length(seq) - 1)
for segment in segments[0]]
_add_trim_segments(segments, seq, kind=OTHER)
return seq
