def test_samplegroup_from_dict_of_dicts(): dict_of_dicts = {"sample1": {"lib1": {"rg1": {"R1": "r1.fq"}}}} samplegroup = SampleGroup([ Sample(id="sample1", libraries=[ Library(id="lib1", readgroups=[ReadGroup(id="rg1", R1="r1.fq")]) ]) ]) assert SampleGroup.from_dict_of_dicts(dict_of_dicts) == samplegroup
def test_file_md5sums(): reads_dir = (Path(FILESDIR) / Path("data")).absolute() samplegroup = SampleGroup([ Sample("s1", [ Library("l1", [ ReadGroup(id="r1", R1=str(reads_dir / Path("R1.fq")), R2=str(reads_dir / Path("R2.fq")), R1_md5="d8e8fca2dc0f896fd7cb4cb0031ba249", R2_md5="126a8a51b9d1bbd07fddc65819a542c3") ]) ]) ]) samplegroup.test_file_checksums()
def test_samplegroup_append_and_access(): sample = Sample(id="blasample") samplegroup = SampleGroup() samplegroup.append_sample(sample) assert samplegroup[0] == sample
def test_incorrect_sample_append(): sample = Sample("sample1") with pytest.raises(TypeError) as error: sample.append_library("lib1") assert error.match("Only library")
def test_sample_append_and_access(): library = Library(id="blalib") sample = Sample(id="blasample") sample.append_library(library) assert sample[0] == library
# SOFTWARE. from pathlib import Path from biowdl_input_converter.samplestructure import Library, ReadGroup, \ Sample, SampleGroup FILESDIR: Path = Path(__file__).parent / Path("files") COMPLETE_WITH_CONTROL_SAMPLEGROUP = SampleGroup([ Sample(id="s1", libraries=[ Library(id="lib1", readgroups=[ ReadGroup(id="rg1", R1="r1.fq", R1_md5="hello", R2="r2.fq", R2_md5="hey") ]) ]), Sample(id="s2", additional_properties=dict(control="s1"), libraries=[ Library(id="lib1", readgroups=[ ReadGroup(id="rg1", R1="r1.fq", R1_md5="aa", R2="r2.fq", R2_md5="bb")