def covered_segments_from_match_parts(match_parts,
in_query=True,
merge_segments_closer=1):
'''Given a list of match_parts it returns the covered segments.
match_part 1 ------- -----> -----------
match_part 2 ------
It returns the list of segments covered by the match parts either in the
query or in the subject.
merge_segments_closer is an integer. Segments closer than the given
number of residues will be merged.
'''
# we collect all start and ends
segments = []
for match_part in match_parts:
if in_query:
start = match_part['query_start']
end = match_part['query_end']
else:
start = match_part['subject_start']
end = match_part['subject_end']
if start > end: # a revesed item
start, end = end, start
segments.append((start, end))
return merge_overlaping_segments(
segments, merge_segments_closer=merge_segments_closer)
def covered_segments_from_match_parts(match_parts, in_query=True,
merge_segments_closer=1):
'''Given a list of match_parts it returns the covered segments.
match_part 1 ------- -----> -----------
match_part 2 ------
It returns the list of segments covered by the match parts either in the
query or in the subject.
merge_segments_closer is an integer. Segments closer than the given
number of residues will be merged.
'''
# we collect all start and ends
segments = []
for match_part in match_parts:
if in_query:
start = match_part['query_start']
end = match_part['query_end']
else:
start = match_part['subject_start']
end = match_part['subject_end']
if start > end: # a revesed item
start, end = end, start
segments.append((start, end))
return merge_overlaping_segments(segments,
merge_segments_closer=merge_segments_closer)
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)
