def _do_trim(self, seq):
'It trims the edges of the given seqs.'
annots = get_annotations(seq)
if not TRIMMING_RECOMMENDATIONS in annots:
return seq
trim_rec = annots[TRIMMING_RECOMMENDATIONS]
# fixing the trimming recommendations
if TRIMMING_RECOMMENDATIONS in annots:
del annots[TRIMMING_RECOMMENDATIONS]
trim_segments = []
for trim_kind in TRIMMING_KINDS:
trim_segments.extend(trim_rec.get(trim_kind, []))
# masking
if self.mask:
seq = _mask_sequence(seq, trim_segments)
else:
# trimming
if trim_segments:
trim_limits = get_longest_complementary_segment(
trim_segments, get_length(seq))
if trim_limits is None:
# there's no sequence left
return None
else:
trim_limits = []
if trim_limits:
seq = slice_seq(seq, trim_limits[0], trim_limits[1] + 1)
return seq
def _do_trim(self, seq):
'It trims the edges of the given seqs.'
annots = get_annotations(seq)
if not TRIMMING_RECOMMENDATIONS in annots:
return seq
trim_rec = annots[TRIMMING_RECOMMENDATIONS]
# fixing the trimming recommendations
if TRIMMING_RECOMMENDATIONS in annots:
del annots[TRIMMING_RECOMMENDATIONS]
trim_segments = []
for trim_kind in TRIMMING_KINDS:
trim_segments.extend(trim_rec.get(trim_kind, []))
# masking
if self.mask:
seq = _mask_sequence(seq, trim_segments)
else:
# trimming
if trim_segments:
trim_limits = get_longest_complementary_segment(
trim_segments, get_length(seq))
if trim_limits is None:
# there's no sequence left
return None
else:
trim_limits = []
if trim_limits:
seq = slice_seq(seq, trim_limits[0], trim_limits[1] + 1)
return seq
def __call__(self, seqrecords):
'It trims the edges of the given seqrecords.'
stats = self._stats
stats[PROCESSED_PACKETS] += 1
mask = self.mask
processed_seqs = []
for seqrecord in seqrecords:
stats[PROCESSED_SEQS] += 1
if not TRIMMING_RECOMMENDATIONS in seqrecord.annotations:
processed_seqs.append(copy_seqrecord(seqrecord))
continue
trim_rec = seqrecord.annotations[TRIMMING_RECOMMENDATIONS]
#fixing the trimming recommendations
if TRIMMING_RECOMMENDATIONS in seqrecord.annotations:
del seqrecord.annotations[TRIMMING_RECOMMENDATIONS]
trim_segments = []
for trim_kind in TRIMMING_KINDS:
trim_segments.extend(trim_rec.get(trim_kind, []))
#masking
if mask:
seqrecord = _mask_sequence(seqrecord, trim_segments)
else:
#trimming
if trim_segments:
trim_limits = get_longest_complementary_segment(
trim_segments, len(seqrecord))
if trim_limits is None:
# there's no sequence left
continue
else:
trim_limits = []
if trim_limits:
seqrecord = seqrecord[trim_limits[0]:trim_limits[1] + 1]
processed_seqs.append(seqrecord)
stats[YIELDED_SEQS] += 1
return processed_seqs
def __call__(self, seqs):
'It trims the edges of the given seqs.'
mask = self.mask
processed_seqs = []
for seq in seqs:
annots = get_annotations(seq)
if not TRIMMING_RECOMMENDATIONS in annots:
processed_seqs.append(copy_seq(seq))
continue
trim_rec = annots[TRIMMING_RECOMMENDATIONS]
# fixing the trimming recommendations
if TRIMMING_RECOMMENDATIONS in annots:
del annots[TRIMMING_RECOMMENDATIONS]
trim_segments = []
for trim_kind in TRIMMING_KINDS:
trim_segments.extend(trim_rec.get(trim_kind, []))
# masking
if mask:
seq = _mask_sequence(seq, trim_segments)
else:
# trimming
if trim_segments:
trim_limits = get_longest_complementary_segment(
trim_segments, get_length(seq))
if trim_limits is None:
# there's no sequence left
continue
else:
trim_limits = []
if trim_limits:
seq = slice_seq(seq, trim_limits[0], trim_limits[1] + 1)
processed_seqs.append(seq)
return processed_seqs
def test_get_longest_complementary():
'It test that we can get the longest complementary segment'
segments = [(0, 200)]
result = get_longest_complementary_segment(segments, seq_len=200)
assert result is None
def test_get_longest_complementary():
'It test that we can get the longest complementary segment'
segments = [(0, 200)]
result = get_longest_complementary_segment(segments, seq_len=200)
assert result is None