def test_unmasked_seq_location_detector():
"it detects the location of the unmasked seq regions"
seq = SeqWithQuality(seq=Seq("AATTaaTTaaTTT"), name="seq")
locations = _get_unmasked_locations(seq)
assert locations[0] == (0, 3)
assert locations[1] == (6, 7)
assert locations[2] == (10, 12)
seq = SeqWithQuality(seq=Seq("AATT"), name="seq")
locations = _get_unmasked_locations(seq)
assert locations[0] == (0, 3)
seq = SeqWithQuality(seq=Seq("aatt"), name="seq")
locations = _get_unmasked_locations(seq)
assert not locations
def test_unmasked_seq_location_detector():
'it detects the location of the unmasked seq regions'
seq = SeqWithQuality(seq=Seq('AATTaaTTaaTTT'), name='seq')
locations = _get_unmasked_locations(seq)
assert locations[0] == (0, 3)
assert locations[1] == (6, 7)
assert locations[2] == (10, 12)
seq = SeqWithQuality(seq=Seq('AATT'), name='seq')
locations = _get_unmasked_locations(seq)
assert locations[0] == (0, 3)
seq = SeqWithQuality(seq=Seq('aatt'), name='seq')
locations = _get_unmasked_locations(seq)
assert not locations
def test_get_matched_regions():
"it tests get_matched_region function"
seq1 = "AATTaatAATTAATtctcTTCtctctctctctcGCGCGCGCGCCC"
seq = SeqWithQuality(seq=Seq(seq1), name="seq")
locations = _get_unmasked_locations(seq)
seqs = list(_get_matched_locations(seq, locations, 3))
assert str(seqs[0].seq) == "AATT"
assert str(seqs[1].seq) == "AATTAAT"
assert str(seqs[2].seq) == "TTC"
assert str(seqs[3].seq) == "GCGCGCGCGCCC"
seqs = list(_get_matched_locations(seq, locations, 5))
assert str(seqs[0].seq) == "AATTAAT"
assert str(seqs[1].seq) == "GCGCGCGCGCCC"
def test_get_matched_regions():
'it tests get_matched_region function'
seq1 = 'AATTaatAATTAATtctcTTCtctctctctctcGCGCGCGCGCCC'
seq = SeqWithQuality(seq=Seq(seq1), name='seq')
locations = _get_unmasked_locations(seq)
seqs = list(_get_matched_locations(seq, locations, 3))
assert str(seqs[0].seq) == 'AATT'
assert str(seqs[1].seq) == 'AATTAAT'
assert str(seqs[2].seq) == 'TTC'
assert str(seqs[3].seq) == 'GCGCGCGCGCCC'
seqs = list(_get_matched_locations(seq, locations, 5))
assert str(seqs[0].seq) == 'AATTAAT'
assert str(seqs[1].seq) == 'GCGCGCGCGCCC'
