def test_require_both():
def f():
pass
g = requires(python_library="pandas", external_binary="top")(f)
assert g.is_disabled is False
g = requires(python_library="tagada5", external_binary="top")(f)
assert g.is_disabled
g = requires(python_library="pandas", external_binary="tagada6")(f)
assert g.is_disabled
g = requires(python_library="tagada7", external_binary="tagada8")(f)
assert g.is_disabled
def test_require_binaries():
def f():
pass
g = requires(external_binary="mv")(f)
assert g.is_disabled is False
# test cache now
g = requires(external_binary="mv")(f)
assert g.is_disabled is False
g = requires(external_binaries=[
"ls",
])(f)
assert g.is_disabled is False
g = requires(external_binaries=[
"ls",
"mv",
])(f)
assert g.is_disabled is False
g = requires(external_binary="tagada1")(f)
assert g.is_disabled
# test cache now
g = requires(external_binary="tagada1")(f)
assert g.is_disabled
g = requires(external_binaries=["rm", "tagada2"])(f)
assert g.is_disabled
def test_require_libraries():
def f():
pass
g = requires(python_library="pandas")(f)
assert g.is_disabled is False
# test cache now
g = requires(python_library="pandas")(f)
assert g.is_disabled is False
g = requires(python_libraries=[
"pip",
])(f)
assert g.is_disabled is False
g = requires(python_libraries=[
"pip",
"pandas",
])(f)
assert g.is_disabled is False
g = requires(python_library="tagada3")(f)
assert g.is_disabled
# test cache now
g = requires(python_library="tagada3")(f)
assert g.is_disabled
g = requires(python_libraries=["urllib3", "tagada4"])(f)
assert g.is_disabled
def test_require_urllib3():
assert requires(python_library="urllib3")(object()).is_disabled is False
def test_require_ls():
assert requires(external_binary="ls")(object()).is_disabled is False
def test_require_faToTwoBit():
assert requires(external_binary="faToTwoBit")(
object()).is_disabled is False
def test_require_conda():
assert requires(external_binary="conda")(object()).is_disabled is False
def test_require_bigWigToBedGraph():
assert requires(external_binary="bigWigToBedGraph")(
object()).is_disabled is False
def test_require_bamCoverage():
assert requires(external_binary="bamCoverage")(
object()).is_disabled is False
def test_require_twoBitToFa():
assert requires(external_binary="twoBitToFa")(
object()).is_disabled is False
def test_require_squizz():
assert requires(external_binary="squizz")(object()).is_disabled is False
def test_require_sambamba():
assert requires(external_binary="sambamba")(object()).is_disabled is False
def test_require_perl():
assert requires(external_binary="perl")(object()).is_disabled is False
def test_require_wheel():
assert requires(python_library="wheel")(object()).is_disabled is False
def test_require_unpigz():
assert requires(external_binary="unpigz")(object()).is_disabled is False
def test_require_xlrd():
assert requires(python_library="xlrd")(object()).is_disabled is False
def test_require_biopython():
assert requires(python_library="biopython")(object()).is_disabled is False
def test_require_bedGraphToBigWig():
assert requires(external_binary="bedGraphToBigWig")(
object()).is_disabled is False
def test_require_mappy():
assert requires(python_library="mappy")(object()).is_disabled is False
def test_require_bunzip2():
assert requires(external_binary="bunzip2")(object()).is_disabled is False
def test_require_pandas():
assert requires(python_library="pandas")(object()).is_disabled is False
def test_require_dsrc():
assert requires(external_binary="dsrc")(object()).is_disabled is False
def test_require_pyexcel_xls():
assert requires(python_library="pyexcel-xls")(
object()).is_disabled is False
def test_require_fastq_dump():
assert requires(external_binary="fastq-dump")(
object()).is_disabled is False
def test_require_pysam():
assert requires(python_library="pysam")(object()).is_disabled is False
def test_require_mawk():
assert requires(external_binary="mawk")(object()).is_disabled is False
with TempFile(suffix=".fasta") as outfile, \
TempFile(suffix=".fasta") as unwrapped:
convert = Fastq2Fasta(infile, outfile.name)
convert(method=method)
Fastq2Fasta.unwrap_fasta(outfile.name,
unwrapped.name,
strip_comment=True)
assert md5(unwrapped.name) == md5out, \
"{} failed".format(method)
@pytest.mark.parametrize("method",
filter(make_in_gz_tester(Fastq2Fasta),
Fastq2Fasta.available_methods))
@pytest.mark.skipif(
requires(external_binary="unpigz")(object()).is_disabled,
reason="missing dependencies",
)
def test_in_gz(method):
for sample_name in [
"test_fastq2fasta_v1", "sample_v2", "sample_v3", "sample_v4"
]:
if method == "GATB" and sample_name in ["sample_v3", "sample_v2"]:
# GATB long headers bug
continue
infile = bioconvert_data("{}.fastq.gz".format(sample_name))
expected_outfile = bioconvert_data("{}.fasta".format(sample_name))
with TempFile(suffix=".fasta") as expected_unwrapped:
Fastq2Fasta.unwrap_fasta(expected_outfile,
expected_unwrapped.name,
