def test_flexible_pedigree_read_from_filesystem(filepath, fixture_dirname):
expected_df = expected_pedigree_df.copy()
expected_df["sample_id"] = expected_df["person_id"]
absolute_filepath = fixture_dirname("pedigrees/{}".format(filepath))
pedigree_df = FamiliesLoader.flexible_pedigree_read(absolute_filepath)
assert pedigree_df.equals(expected_df)
def test_ped_prepare_simple(test_config, fake_ped_file):
test_config.person.role.mapping = "INTERNAL"
prep = PreparePersons(test_config)
ped_df = FamiliesLoader.flexible_pedigree_read(fake_ped_file)
assert ped_df is not None
ped_df = prep.prepare_pedigree(ped_df)
prep.save_pedigree(ped_df)
def test_flexible_pedigree_read(infile, pedigree):
loaded_pedigree = FamiliesLoader.flexible_pedigree_read(infile, sep="\t")
print(loaded_pedigree)
columns = [
"family_id",
"person_id",
"dad_id",
"mom_id",
"sex",
"status",
"role",
"layout",
"sample_id",
]
for column in columns:
assert (
loaded_pedigree[column].values == pedigree[column].values).all()
def test_flexible_pedigree_read_do_not_override_sample_id_column(
fixture_dirname, ):
expected_df = expected_pedigree_df.copy()
expected_df["sample_id"] = [
"f1_father",
"f1_mother",
"f1_sibling1",
"f1_proband",
"f1_sibling2",
"f2_mother",
"f2_father",
"f2_proband",
"f2_sibling1",
]
absolute_filepath = fixture_dirname("pedigrees/pedigree_E.ped")
pedigree_df = FamiliesLoader.flexible_pedigree_read(absolute_filepath)
assert pedigree_df.equals(expected_df)
def test_flexible_pedigree_read_additional_columns(fixture_dirname):
expected_df = expected_pedigree_df.copy()
expected_df["phenotype"] = [
"healthy",
"healthy",
"healthy",
"disease",
"disease",
"healthy",
"healthy",
"disease",
"healthy",
]
expected_df["sample_id"] = expected_df["person_id"]
absolute_filepath = fixture_dirname("pedigrees/pedigree_D.ped")
pedigree_df = FamiliesLoader.flexible_pedigree_read(absolute_filepath)
assert pedigree_df.equals(expected_df)
def test_flexible_pedigree_read_no_header(fixture_dirname):
expected_df = expected_pedigree_df.copy()
expected_df["sample_id"] = expected_df["person_id"]
absolute_filepath = fixture_dirname("pedigrees/pedigree_no_header.ped")
pedigree_df = FamiliesLoader.flexible_pedigree_read(
absolute_filepath,
ped_no_header=True,
ped_family=0,
ped_person=1,
ped_dad=2,
ped_mom=3,
ped_sex=4,
ped_status=5,
ped_role=6,
)
print(pedigree_df)
print(expected_df)
assert pedigree_df.equals(expected_df)
def fake_families(fixture_dirname):
ped_df = FamiliesLoader.flexible_pedigree_read(
fixture_dirname("denovo_import/fake_pheno.ped"))
fake_families = FamiliesData.from_pedigree_df(ped_df)
return fake_families
def build_pedigree(self, pedfile):
ped_df = FamiliesLoader.flexible_pedigree_read(pedfile)
ped_df = self.prepare_pedigree(ped_df)
self.save_pedigree(ped_df)
self.pedigree_df = ped_df
return ped_df