def test_check_is_pair_4b():
read1 = Sequence(name='seq/1', sequence='AAA')
read2 = Sequence(name='seq/2', quality='###', sequence='AAA')
try:
check_is_pair(read1, read2)
assert False # check_is_pair should fail here.
except ValueError:
pass
def test_SanitizedFastxParser_invalid(create_fastx):
'''Test that parser detects invalid sequence'''
expected = [Sequence('seq1/1', 'XXX'), Sequence('seq1/2', 'A' * 4)]
parser = SanitizedFastxParser(create_fastx(expected))
result = list(parser)
assert parser.n_bad == 1
assert len(result) == 1
assert result[0].sequence == 'A' * 4
def test_SanitizedFastxParser_no_convert_Ns(create_fastx):
expected = [Sequence('seq1/1', 'N' * 5), Sequence('seq1/2', 'N' * 4)]
parser = SanitizedFastxParser(create_fastx(expected),
alphabet='DNAN_SIMPLE',
convert_n=False)
result = list(parser)
assert parser.n_bad == 0
assert len(result) == 2
assert result[0].sequence == 'N' * 5
assert result[1].sequence == 'N' * 4
def test_SanitizedFastxParser_convert_Ns(create_fastx):
'''Test that A's are converted to N's'''
expected = [Sequence('seq1/1', 'N' * 5), Sequence('seq1/2', 'N' * 4)]
parser = SanitizedFastxParser(create_fastx(expected),
alphabet='DNAN_SIMPLE')
result = list(parser)
assert parser.n_bad == 0
assert len(result) == 2
assert result[0].sequence == 'A' * 5
assert result[1].sequence == 'A' * 4
def test_FastxParser(create_fastx):
expected = [
Sequence('seq1/1', 'A' * 5),
Sequence('seq1/2', 'A' * 4),
Sequence('seq2/1', 'A' * 5),
Sequence('seq3/1', 'A' * 3),
Sequence('seq3/2', 'A' * 5)
]
parser = FastxParser(create_fastx(expected))
result = list(parser)
assert len(expected) == len(result)
assert all((x == y) for x, y in zip(expected, result))
def test_SanitizedFastxParser_lowercase(create_fastx):
reads = [
Sequence('seq1/1', 'acgtn'),
Sequence('seq1/2', 'AcGtN'),
Sequence('seq1/2', 'aCgTn')
]
parser = SanitizedFastxParser(create_fastx(reads), convert_n=False)
result = list(parser)
assert result[0].sequence == 'ACGTN'
assert result[1].sequence == 'ACGTN'
assert result[2].sequence == 'ACGTN'
def test_init_sequence_only(self):
s = Sequence(sequence=self.sequence)
assert s.name is None
assert s.sequence is None
assert s.quality is None
assert s.description is None
assert s.cleaned_seq is None
def test_init_name_and_sequence(self):
s = Sequence(name=self.name, sequence=self.sequence)
assert s.name == self.name
assert s.sequence == self.sequence
assert s.quality is None
assert s.description is None
assert s.cleaned_seq == self.sequence
def test_init_with_cleaned_seq(self):
s = Sequence(name=self.name,
sequence=self.sequence,
cleaned_seq=self.cleaned)
assert s.name == self.name
assert s.sequence == self.sequence
assert s.quality is None
assert s.description is None
assert s.cleaned_seq == self.cleaned
def testRequirePairedAndMinLength_NeitherPass(self, parser, create_fastx):
reads = [
Sequence('seq1/1', 'A' * 5),
Sequence('seq1/2', 'A' * 4),
Sequence('seq3/1', 'A' * 3),
Sequence('seq3/2', 'A' * 3)
]
reader = BrokenPairedReader(parser(create_fastx(reads)),
min_length=4,
require_paired=True)
result = []
for n, paired, first, second in reader:
result.append((first, second))
assert n == 0
assert len(result) == 1
l, r = result[0]
assert l == reads[0]
assert r == reads[1]
def test_check_is_pair_7():
read1 = Sequence(name='seq/2', sequence='AAA')
read2 = Sequence(name='seq/1', sequence='AAA')
assert not check_is_pair(read1, read2)
def test_check_is_pair_3_fa():
read1 = Sequence(name='seq 1::', sequence='AAA')
read2 = Sequence(name='seq 2::', sequence='AAA')
assert check_is_pair(read1, read2)
def test_check_is_pair_3_broken_fq_2():
read1 = Sequence(name='seq 1::', quality='###', sequence='AAA')
read2 = Sequence(name='seq', quality='###', sequence='AAA')
assert not check_is_pair(read1, read2)
def test_check_is_pair_2():
read1 = Sequence(name='seq/1', quality='###', sequence='AAA')
read2 = Sequence(name='seq/2', quality='###', sequence='AAA')
assert check_is_pair(read1, read2)
class Test_BrokenPairedReader(object):
reads = [
Sequence(name='seq1/1', sequence='A' * 5),
Sequence(name='seq1/2', sequence='A' * 4),
Sequence(name='seq2/1', sequence='A' * 5),
Sequence(name='seq3/1', sequence='A' * 3),
Sequence(name='seq3/2', sequence='A' * 5)
]
@pytest.mark.parametrize("parser", [FastxParser, SanitizedFastxParser])
def testDefault(self, parser, create_fastx):
x, n, m = gather_paired(parser(create_fastx(self.reads)), min_length=1)
expected = [('seq1/1', 'seq1/2'), ('seq2/1', None),
('seq3/1', 'seq3/2')]
assert x == expected, x
assert m == 3
assert n == 3, n
@pytest.mark.parametrize("parser", [FastxParser, SanitizedFastxParser])
def testMinLength(self, parser, create_fastx):
x, n, m = gather_paired(parser(create_fastx(self.reads)), min_length=3)
expected = [('seq1/1', 'seq1/2'), ('seq2/1', None),
('seq3/1', 'seq3/2')]
assert x == expected, x
assert m == 3
assert n == 3, n
@pytest.mark.parametrize("parser", [FastxParser, SanitizedFastxParser])
def testMinLength_2(self, parser, create_fastx):
x, n, m = gather_paired(parser(create_fastx(self.reads)), min_length=4)
expected = [('seq1/1', 'seq1/2'), ('seq2/1', None), (None, 'seq3/2')]
assert x == expected, x
assert m == 3
assert n == 3, n
@pytest.mark.parametrize("parser", [FastxParser, SanitizedFastxParser])
def testForceSingle(self, parser, create_fastx):
x, n, m = gather_paired(parser(create_fastx(self.reads)),
force_single=True)
expected = [('seq1/1', None), ('seq1/2', None), ('seq2/1', None),
('seq3/1', None), ('seq3/2', None)]
assert x == expected, x
assert m == 5
assert n == 4, n
@pytest.mark.parametrize("parser", [FastxParser, SanitizedFastxParser])
def testForceSingleAndMinLength(self, parser, create_fastx):
x, n, m = gather_paired(parser(create_fastx(self.reads)),
min_length=5,
force_single=True)
expected = [('seq1/1', None), ('seq2/1', None), ('seq3/2', None)]
assert x == expected, x
assert m == 3, m
assert n == 2, n
@pytest.mark.parametrize("parser", [FastxParser, SanitizedFastxParser])
def testRequirePairedAndMinLength_HalfPass(self, parser, create_fastx):
reads = [
Sequence('seq1/1', 'A' * 5),
Sequence('seq1/2', 'A' * 4),
Sequence('seq3/1', 'A' * 3),
Sequence('seq3/2', 'A' * 5)
]
reader = BrokenPairedReader(parser(create_fastx(reads)),
min_length=4,
require_paired=True)
result = []
for n, paired, first, second in reader:
result.append((first, second))
assert len(result) == 1
assert n == 0
l, r = result[0]
assert l == reads[0]
assert r == reads[1]
@pytest.mark.parametrize("parser", [FastxParser, SanitizedFastxParser])
def testRequirePairedAndMinLength_SwappedHalfPass(self, parser,
create_fastx):
reads = [
Sequence('seq1/1', 'A' * 5),
Sequence('seq1/2', 'A' * 4),
Sequence('seq3/1', 'A' * 5),
Sequence('seq3/2', 'A' * 3)
]
reader = BrokenPairedReader(parser(create_fastx(reads)),
min_length=4,
require_paired=True)
result = []
for n, paired, first, second in reader:
result.append((first, second))
assert n == 0
assert len(result) == 1
l, r = result[0]
assert l == reads[0]
assert r == reads[1]
@pytest.mark.parametrize("parser", [FastxParser, SanitizedFastxParser])
def testRequirePairedAndMinLength_NeitherPass(self, parser, create_fastx):
reads = [
Sequence('seq1/1', 'A' * 5),
Sequence('seq1/2', 'A' * 4),
Sequence('seq3/1', 'A' * 3),
Sequence('seq3/2', 'A' * 3)
]
reader = BrokenPairedReader(parser(create_fastx(reads)),
min_length=4,
require_paired=True)
result = []
for n, paired, first, second in reader:
result.append((first, second))
assert n == 0
assert len(result) == 1
l, r = result[0]
assert l == reads[0]
assert r == reads[1]
@pytest.mark.parametrize("parser", [FastxParser, SanitizedFastxParser])
def testRequirePairedAndMinLength_SwappedNeitherPass(
self, parser, create_fastx):
reads = [
Sequence('seq1/1', 'A' * 3),
Sequence('seq1/2', 'A' * 3),
Sequence('seq3/1', 'A' * 5),
Sequence('seq3/2', 'A' * 5)
]
reader = BrokenPairedReader(parser(create_fastx(reads)),
min_length=4,
require_paired=True)
result = []
for n, paired, first, second in reader:
result.append((first, second))
assert n == 0
assert len(result) == 1
l, r = result[0]
assert l == reads[2]
assert r == reads[3]