def test_cnv_loader_alt_best_state(fixture_dirname, genomes_db_2013):
families_file = fixture_dirname("backends/cnv_ped.txt")
families = FamiliesLoader.load_simple_families_file(families_file)
assert families is not None
variants_file = fixture_dirname(
"backends/cnv_variants_alt_1_best_state.txt")
loader = CNVLoader(families,
variants_file,
genomes_db_2013.get_genome(),
params={
"cnv_chrom": "Chr",
"cnv_start": "Start",
"cnv_end": "Stop",
"cnv_variant_type": "Del/Dup",
"cnv_plus_values": ["Dup", "Dup_Germline"],
"cnv_minus_values": ["Del", "Del_Germline"],
"cnv_person_id": "personId"
})
assert loader is not None
svs = []
fvs = []
for sv, _fvs in loader.full_variants_iterator():
print(sv, fvs)
svs.append(sv)
for fv in _fvs:
fvs.append(fv)
assert len(svs) == 1
assert len(fvs) == 4
print(fvs[0].best_state)
def test_extra_attributes_serialization_deserialization(
fixtures_gpf_instance, fixture_dirname):
families_data = FamiliesLoader.load_simple_families_file(
fixture_dirname("backends/iossifov_extra_attrs.ped"))
loader = DenovoLoader(
families_data, fixture_dirname("backends/iossifov_extra_attrs.tsv"),
fixtures_gpf_instance.get_genome()
)
main_schema = loader.get_attribute("annotation_schema")
extra_attributes = loader.get_attribute("extra_attributes")
serializer = AlleleParquetSerializer(main_schema, extra_attributes)
it = loader.full_variants_iterator()
variant = next(it)[1][0]
print(variant.gt)
summary_blobs = serializer.serialize_summary_data(variant.alleles)
scores_blob = serializer.serialize_scores_data(variant.alleles)
variant_blob = serializer.serialize_family_variant(
variant.alleles, summary_blobs, scores_blob
)
extra_blob = serializer.serialize_extra_attributes(variant)
family = variant.family
fv = serializer.deserialize_family_variant(
variant_blob, family, extra_blob)
assert fv.get_attribute("someAttr")[0] == "asdf"
def test_cnv_loader_alt_2(fixture_dirname, genomes_db_2013):
families_file = fixture_dirname("backends/cnv_ped.txt")
families = FamiliesLoader.load_simple_families_file(families_file)
assert families is not None
variants_file = fixture_dirname("backends/cnv_variants_alt_2.txt")
loader = CNVLoader(families,
variants_file,
genomes_db_2013.get_genome(),
params={
"cnv_location": "location",
"cnv_variant_type": "variant",
"cnv_plus_values": ["duplication"],
"cnv_minus_values": ["deletion"],
"cnv_person_id": "personId"
})
assert loader is not None
svs = []
fvs = []
for sv, _fvs in loader.full_variants_iterator():
print(sv, fvs)
svs.append(sv)
for fv in _fvs:
fvs.append(fv)
assert len(svs) == 29
assert len(fvs) == 30
def test_load_family_simple(fixture_name, temp_filename, fixture_dirname):
family_filename = fixture_dirname(fixture_name)
assert os.path.exists(family_filename)
families = FamiliesLoader.load_simple_families_file(family_filename)
assert families is not None
FamiliesLoader.save_pedigree(families, temp_filename)
families1 = FamiliesLoader.load_pedigree_file(temp_filename)
assert set(families.keys()) == set(families1.keys())
def test_cnv_loader(fixture_dirname, genomes_db_2013):
families_file = fixture_dirname("backends/cnv_ped.txt")
families = FamiliesLoader.load_simple_families_file(families_file)
assert families is not None
variants_file = fixture_dirname("backends/cnv_variants.txt")
loader = CNVLoader(families, variants_file, genomes_db_2013.get_genome())
assert loader is not None
svs = []
for sv, fvs in loader.full_variants_iterator():
print(sv, fvs)
svs.append(sv)
assert len(svs) == 12
def denovo_extra_attr_loader(
fixture_dirname, genome_2013, annotation_pipeline_internal):
families_filename = fixture_dirname("backends/iossifov_extra_attrs.ped")
variants_filename = fixture_dirname("backends/iossifov_extra_attrs.tsv")
families = FamiliesLoader.load_simple_families_file(families_filename)
variants_loader = DenovoLoader(
families, variants_filename, genome_2013)
variants_loader = AnnotationPipelineDecorator(
variants_loader, annotation_pipeline_internal
)
return variants_loader
def dae_transmitted(dae_transmitted_config, genome_2013,
annotation_pipeline_internal):
# ped_df = FamiliesLoader.load_simple_family_file(
# dae_transmitted_config.family_filename
# )
families = FamiliesLoader.load_simple_families_file(
dae_transmitted_config.family_filename)
variants_loader = DaeTransmittedLoader(
families,
dae_transmitted_config.summary_filename,
# dae_transmitted_config.toomany_filename,
genome=genome_2013,
regions=None,
)
variants_loader = AnnotationPipelineDecorator(
variants_loader, annotation_pipeline_internal)
return variants_loader