def test_quality_raises_on_0_return(new_pipegraph):
with pytest.raises(ValueError):
fastq2.QualityFilter(lambda qual, seq: 0).generate_aligner_input(
"test.fastq",
[str(get_sample_data(Path("mbf_align/sample_a/a.fastq")))],
False,
)
def test_quality_filter_depends_on_function_invariant(new_pipegraph):
def f(qual, seq):
return True
x = fastq2.QualityFilter(f)
deps = x.get_dependencies("test.fastq")
assert isinstance(deps[0], ppg.FunctionInvariant)
assert deps[0].function is f
def test_quality_filter_positive_integer(self):
test = b"""@SEQ_ID_1
AATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
AcAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@SEQ_ID_2
TATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@SEQ_ID_3
AAAATGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@SEQ_ID_4
CATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA
"""
should = b"""@SEQ_ID_1
AATTT
+
AcAAA
@SEQ_ID_3
AAAAT
+
BBBBB
"""
try:
with open("test_quality_filter_positive_integer.fastq",
"wb") as op:
op.write(test)
def f(qual, seq):
if seq.startswith(b"A"): # keep the first 5 bases
return 5
else:
return False
x = fastq2.QualityFilter(f)
x.generate_aligner_input(
"test_quality_filter_positive_integer.out.fastq",
["test_quality_filter_positive_integer.fastq"],
False,
)
with open("test_quality_filter_positive_integer.out.fastq",
"rb") as op:
was = op.read()
assert should == was
finally:
if os.path.exists(
"test_quality_filter_positive_integer.out.fastq"):
os.unlink("test_quality_filter_positive_integer.out.fastq")
def test_quality_filter_tuple(self):
test = b"""@SEQ_ID_1
AATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
AcAAAAghAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@SEQ_ID_2
TATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@SEQ_ID_3
AAAATGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBcBBBBB
@SEQ_ID_4
CATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA
"""
should = b"""@SEQ_ID_1
GGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCAC
+
ghAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@SEQ_ID_3
GGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCAC
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBc
"""
try:
with open("test_quality_filter_tuple.fastq", "wb") as op:
op.write(test)
def f(qual, seq):
if seq.startswith(b"A"):
return (6, -5)
else:
return False
x = fastq2.QualityFilter(f)
x.generate_aligner_input(
"test_quality_filter_tuple.out.fastq",
["test_quality_filter_tuple.fastq"],
False,
)
with open("test_quality_filter_tuple.out.fastq", "rb") as op:
was = op.read()
assert should == was
finally:
if os.path.exists("test_quality_filter_tuple.out.fastq"):
os.unlink("test_quality_filter_tuple.out.fastq")
def test_read_creator_must_be_fastq_right_now(new_pipegraph):
with pytest.raises(ValueError):
fastq2.Straight().generate_aligner_input(
"test.fastq",
[str(get_sample_data(Path("mbf_align/sample_a)/a.fastq")))],
False,
"fail",
)
with pytest.raises(ValueError):
fastq2.Filtered(lambda seq, qual, name: True).generate_aligner_input(
"test.fastq",
[str(get_sample_data(Path("mbf_align/sample_a)/a.fastq")))],
False,
"fail",
)
with pytest.raises(ValueError):
fastq2.QualityFilter(lambda qual, seq: True).generate_aligner_input(
"test.fastq",
[str(get_sample_data(Path("mbf_align/sample_a)/a.fastq")))],
False,
"fail",
)