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,