def test_forward_words():
'It test that we can match words against in the same orientation'
seq = 'gCACAggTGTGggTATAgg'
seq = SeqWithQuality(seq=Seq(seq))
result = match_words(seq, ['CACA', 'TATA', 'KK'])[0]
assert result['query'] == seq
#The match por CACA
match = result['matches'][0]
assert match['subject'] == 'CACA'
assert match['start'] == 1
assert match['end'] == 10
assert len(match['match_parts']) == 2
#the reverse match part
assert match['match_parts'][1] == {'query_start':7,
'query_end':10,
'query_strand':1,
'subject_start':0,
'subject_end':3,
'subject_strand':-1}
#The match por TATA
match = result['matches'][1]
assert match['subject'] == 'TATA'
assert match['start'] == 13
assert match['end'] == 16
assert len(match['match_parts']) == 2
#No matches for KK
assert len(result['matches']) == 2
def strip_words_by_matching(sequence):
"""It strips the given words from a sequence.
It returns a striped sequence with the longest segment without the
words.
"""
if sequence is None:
return None
if not words:
return sequence
alignments = match_words(sequence, words)
if not alignments:
return sequence
locations = _get_non_matched_locations(alignments)
segments = _get_longest_non_matched_seq_region_limits(sequence, locations)
if segments is None:
return None
segments = _get_non_matched_from_matched_locations([segments], len(sequence))
_add_trim_segments(segments, sequence)
return sequence
