def test_get_cutouts_basic():
intervals = Localizer(seedsize=10)
intervals.add_seed_match('bogus-genome-chr2', 10)
refrstream = open(data_file('bogus-genome/refr.fa'), 'r')
seqs = kevlar.seqio.parse_seq_dict(refrstream)
cutouts = list(intervals.get_cutouts(refrseqs=seqs))
assert len(cutouts) == 1
assert cutouts[0].defline == 'bogus-genome-chr2_10-20'
assert cutouts[0].sequence == 'GTTACATTAC'
def test_get_cutouts_large_span():
refrstream = open(data_file('simple-genome-ctrl1.fa'), 'r')
seqs = kevlar.seqio.parse_seq_dict(refrstream)
intervals = Localizer(seedsize=21, delta=25)
intervals.add_seed_match('simple', 100)
intervals.add_seed_match('simple', 200)
cutouts = intervals.get_cutouts(refrseqs=seqs, clusterdist=50)
deflines = [c.defline for c in cutouts]
assert deflines == ['simple_75-146', 'simple_175-246']
intervals = Localizer(seedsize=21, delta=50)
intervals.add_seed_match('simple', 100)
intervals.add_seed_match('simple', 200)
cutouts = intervals.get_cutouts(refrseqs=seqs, clusterdist=100)
deflines = [c.defline for c in cutouts]
assert deflines == ['simple_50-271']
def test_get_cutouts_basic_2():
intervals = Localizer(seedsize=21)
intervals.add_seed_match('simple', 49)
intervals.add_seed_match('simple', 52)
intervals.add_seed_match('simple', 59)
refrstream = open(data_file('simple-genome-ctrl1.fa'), 'r')
seqs = kevlar.seqio.parse_seq_dict(refrstream)
cutouts = list(intervals.get_cutouts(refrseqs=seqs, delta=5))
assert len(cutouts) == 1
assert cutouts[0].defline == 'simple_44-85'
assert cutouts[0].sequence == 'AATACTATGCCGATTTATTCTTACACAATTAAATTGCTAGT'
def test_get_cutouts_basic_3():
intervals = Localizer(seedsize=21, delta=10)
intervals.add_seed_match('simple', 40)
intervals.add_seed_match('simple', 80)
intervals.add_seed_match('simple', 120)
intervals.add_seed_match('simple', 500)
refrstream = open(data_file('simple-genome-ctrl1.fa'), 'r')
seqs = kevlar.seqio.parse_seq_dict(refrstream)
cutouts = list(intervals.get_cutouts(refrseqs=seqs, clusterdist=None))
assert len(cutouts) == 1
assert cutouts[0].defline == 'simple_30-531'
assert len(cutouts[0].sequence) == 501
def test_localizer_incl_excl():
intervals = Localizer(seedsize=25)
intervals.add_seed_match('1', 100)
intervals.add_seed_match('1', 120)
intervals.add_seed_match('12', 200)
intervals.add_seed_match('12', 209)
intervals.add_seed_match('12', 213)
intervals.add_seed_match('X', 1234)
intervals.add_seed_match('X', 1245)
intervals.add_seed_match('Un', 13579)
intervals.add_seed_match('Un', 13597)
testint = [c.interval for c in intervals.get_cutouts()]
assert sorted(testint) == [
('1', 100, 145),
('12', 200, 238),
('Un', 13579, 13622),
('X', 1234, 1270),
]
intervals.exclpattern = 'Un'
testint = [c.interval for c in intervals.get_cutouts()]
assert sorted(testint) == [
('1', 100, 145),
('12', 200, 238),
('X', 1234, 1270),
]
intervals.inclpattern = r'^\d+$'
testint = [c.interval for c in intervals.get_cutouts()]
assert sorted(testint) == [
('1', 100, 145),
('12', 200, 238),
]
def test_localizer_simple():
intervals = Localizer(seedsize=25)
assert list(intervals.get_cutouts()) == []
intervals.add_seed_match('chr1', 100)
intervals.add_seed_match('chr1', 115)
intervals.add_seed_match('chr2', 200)
intervals.add_seed_match('chr2', 205)
intervals.add_seed_match('chr2', 207)
intervals.add_seed_match('chr2', 235008)
intervals.add_seed_match('chr2', 235075)
testint = [c.interval for c in intervals.get_cutouts()]
print('DEBUG', testint)
assert testint == [('chr1', 100, 140), ('chr2', 200, 232),
('chr2', 235008, 235100)]
def test_extract_regions_boundaries():
refrstream = open(data_file('simple-genome-ctrl1.fa'), 'r')
seqs = kevlar.seqio.parse_seq_dict(refrstream)
intervals = Localizer(seedsize=31)
intervals.add_seed_match('simple', 15)
cutouts = list(intervals.get_cutouts(refrseqs=seqs, delta=20))
assert len(cutouts) == 1
assert cutouts[0].defline == 'simple_0-66'
intervals = Localizer(seedsize=31)
intervals.add_seed_match('simple', 925)
intervals.add_seed_match('simple', 955)
intervals.add_seed_match('simple', 978)
cutouts = list(intervals.get_cutouts(refrseqs=seqs, delta=20))
assert len(cutouts) == 1
assert cutouts[0].defline == 'simple_905-1000'
def test_get_cutouts_missing_seq():
intervals = Localizer(seedsize=21)
intervals.add_seed_match('simple', 100)
intervals.add_seed_match('simple', 200)
intervals.add_seed_match('TheCakeIsALie', 42)
intervals.add_seed_match('TheCakeIsALie', 100)
intervals.add_seed_match('TheCakeIsALie', 77)
refrstream = open(data_file('simple-genome-ctrl1.fa'), 'r')
seqs = kevlar.seqio.parse_seq_dict(refrstream)
with pytest.raises(KevlarRefrSeqNotFoundError, match=r'TheCakeIsALie'):
list(intervals.get_cutouts(refrseqs=seqs))