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 _mask_sequence(seqrecord, segments):
'It masks the given segments of the sequence'
if not segments:
return seqrecord
segments = merge_overlaping_segments(segments)
segments = get_all_segments(segments, len(seqrecord))
seq = str(seqrecord.seq)
new_seq = ''
for segment in segments:
start = segment[0][0]
end = segment[0][1] + 1
seq_ = seq[start:end]
if segment[1]:
seq_ = seq_.lower()
new_seq += seq_
return copy_seqrecord(seqrecord, seq=Seq(new_seq,
alphabet=seqrecord.seq.alphabet))
