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_incorrect_samplegroup_append():
samplegroup = SampleGroup()
with pytest.raises(TypeError) as error:
samplegroup.append_sample("sample1")
assert error.match("Only sample ")
def test_samplegroup_append_and_access():
sample = Sample(id="blasample")
samplegroup = SampleGroup()
samplegroup.append_sample(sample)
assert samplegroup[0] == sample
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")
])
])
])
WITHOUT_MD5_SAMPLEGROUP = SampleGroup([
Sample(id="s1",