def test_get_all_segments():
'Give a list of discontinious segments we get all segments'
segments = get_all_segments([(0, 10), (15, 20)], 30)
assert segments == [((0, 10), True), ((11, 14), False),
((15, 20), True), ((21, 29), False)]
segments = get_all_segments([(15, 20)], 30)
assert segments == [((0, 14), False), ((15, 20), True),
((21, 29), False)]
segments = get_all_segments([(15, 29)], 30)
assert segments == [((0, 14), False), ((15, 29), True)]
def test_get_all_segments():
'Give a list of discontinious segments we get all segments'
segments = get_all_segments([(0, 10), (15, 20)], 30)
assert segments == [((0, 10), True), ((11, 14), False),
((15, 20), True), ((21, 29), False)]
segments = get_all_segments([(15, 20)], 30)
assert segments == [((0, 14), False),
((15, 20), True), ((21, 29), False)]
segments = get_all_segments([(15, 29)], 30)
assert segments == [((0, 14), False), ((15, 29), True)]
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))
def _mask_sequence(seq, segments):
'It masks the given segments of the sequence'
if not segments:
return seq
segments = merge_overlaping_segments(segments)
segments = get_all_segments(segments, get_length(seq))
str_seq = get_str_seq(seq)
new_seq = ''
for segment in segments:
start = segment[0][0]
end = segment[0][1] + 1
str_seq_ = str_seq[start:end]
if segment[1]:
str_seq_ = str_seq_.lower()
new_seq += str_seq_
if seq.kind == SEQRECORD:
new_seq = Seq(new_seq, alphabet=seq.object.seq.alphabet)
return copy_seq(seq, seq=new_seq)
def _mask_sequence(seq, segments):
'It masks the given segments of the sequence'
if not segments:
return seq
segments = merge_overlaping_segments(segments)
segments = get_all_segments(segments, get_length(seq))
str_seq = get_str_seq(seq)
new_seq = ''
for segment in segments:
start = segment[0][0]
end = segment[0][1] + 1
str_seq_ = str_seq[start:end]
if segment[1]:
str_seq_ = str_seq_.lower()
new_seq += str_seq_
if seq.kind == SEQRECORD:
new_seq = Seq(new_seq, alphabet=seq.object.seq.alphabet)
return copy_seq(seq, seq=new_seq)
