def _get_matched_locations(seq, locations, min_length):
"It returns a seq iterator from a seq. To split the seq it uses the"
for i, (start, end) in enumerate(locations):
seq1 = seq.seq[start : end + 1]
if len(seq1) < min_length:
continue
if seq.qual is not None:
qual = seq.qual[start : end + 1]
else:
qual = None
if seq.name is not None:
name = "%s_%d" % (seq.name, i + 1)
yield copy_seq_with_quality(seq, seq=seq1, qual=qual, name=name)
def _mask_sequence(sequence, segments):
"It mask the given segments of the sequence"
if not segments:
return sequence
segments = _get_all_segments(segments, len(sequence))
seq = str(sequence.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_seq_with_quality(sequence, seq=Seq(new_seq, sequence.seq.alphabet))
def mapper(sequence):
"the mapper"
if not sequence:
return None
recoded_seq = double_encode_color_space(str(sequence.seq))
return copy_seq_with_quality(sequence, Seq(recoded_seq))
