def test_flexible_denovo_vcf_best_state(fixture_dirname, gpf_instance_2019,
temp_dirname, genomes_db_2019):
pedigree_filename = fixture_dirname(
"flexible_short/flexible_short_families.ped")
denovo_filename = fixture_dirname(
"flexible_short/flexible_short_vcf_best_state.txt")
genotype_storage_id = "test_filesystem"
study_id = "test_flexible_denovo_vcf_best_state"
storage_config = getattr(gpf_instance_2019.dae_config.storage,
genotype_storage_id)
assert storage_config.storage_type == "filesystem"
genotype_storage = FilesystemGenotypeStorage(storage_config,
genotype_storage_id)
assert genotype_storage
argv = [
pedigree_filename,
"--id",
study_id,
"--skip-reports",
"--denovo-file",
denovo_filename,
"--denovo-family-id",
"familyId",
"--denovo-best-state",
"bestState",
"--denovo-location",
"location",
"--denovo-ref",
"reference",
"--denovo-alt",
"alternative",
"--genotype-storage",
genotype_storage_id,
"-o",
temp_dirname,
]
main(argv, gpf_instance_2019)
storage_config = getattr(gpf_instance_2019.dae_config.storage,
genotype_storage_id)
assert storage_config.storage_type == "filesystem"
gpf_instance_2019.reload()
study = gpf_instance_2019.get_genotype_data(study_id)
assert study is not None
vs = list(study.query_variants())
assert_proper_flexible_short_variants(vs)
def test_import_iossifov2014_into_genotype_storage(
genotype_storage_id,
storage_type,
genomes_db_2013,
fixture_dirname,
default_dae_config,
gpf_instance_2013,
temp_dirname,
):
pedigree_filename = fixture_dirname(
"dae_iossifov2014/iossifov2014_families.ped")
denovo_filename = fixture_dirname("dae_iossifov2014/iossifov2014.txt")
study_id = f"test_denovo_iossifov2014_{genotype_storage_id}"
argv = [
pedigree_filename,
"--id",
study_id,
"--skip-reports",
"--denovo-file",
denovo_filename,
"--denovo-location",
"location",
"--denovo-variant",
"variant",
"--denovo-family-id",
"familyId",
"--denovo-best-state",
"bestState",
"--genotype-storage",
genotype_storage_id,
"-o",
temp_dirname,
]
main(argv, gpf_instance_2013)
gpf_instance_2013.reload()
study = gpf_instance_2013.get_genotype_data(study_id)
assert study is not None
vs = list(study.query_variants())
assert len(vs) == 16
vs = list(study.query_variants(effect_types=["splice-site"]))
assert len(vs) == 9
vs = list(study.query_variants(effect_types=["no-frame-shift"]))
assert len(vs) == 2
def test_import_comp_all_into_genotype_storage(
genotype_storage_id,
storage_type,
genomes_db_2013,
fixture_dirname,
default_dae_config,
gpf_instance_2013,
temp_dirname,
):
pedigree_filename = fixture_dirname("study_import/comp.ped")
vcf_filename = fixture_dirname("study_import/comp.vcf")
denovo_filename = fixture_dirname("study_import/comp.tsv")
study_id = f"test_comp_all_{genotype_storage_id}"
argv = [
pedigree_filename,
"--id",
study_id,
"--vcf-denovo-mode",
"possible_denovo",
"--vcf-omission-mode",
"possible_omission",
"--vcf-files",
vcf_filename,
"--denovo-file",
denovo_filename,
"--denovo-location",
"location",
"--denovo-variant",
"variant",
"--denovo-family-id",
"familyId",
"--denovo-best-state",
"bestState",
"--genotype-storage",
genotype_storage_id,
"-o",
temp_dirname,
]
main(argv, gpf_instance_2013)
gpf_instance_2013.reload()
study = gpf_instance_2013.get_genotype_data(study_id)
assert study is not None
vs = list(study.query_variants())
assert len(vs) == 35
def test_flexible_denovo_dae_person(fixture_dirname, gpf_instance_2019,
temp_dirname, genomes_db_2019):
pedigree_filename = fixture_dirname(
"flexible_short/flexible_short_families.ped")
denovo_filename = fixture_dirname(
"flexible_short/flexible_short_dae_person.txt")
genotype_storage_id = "test_filesystem"
study_id = "test_flexible_denovo_dae_person"
storage_config = getattr(gpf_instance_2019.dae_config.storage,
genotype_storage_id)
assert storage_config.storage_type == "filesystem"
genotype_storage = FilesystemGenotypeStorage(storage_config,
genotype_storage_id)
assert genotype_storage
argv = [
pedigree_filename,
"--id",
study_id,
"--skip-reports",
"--denovo-file",
denovo_filename,
"--denovo-variant",
"variant",
"--denovo-person-id",
"person_id",
"--genotype-storage",
genotype_storage_id,
"-o",
temp_dirname,
]
main(argv, gpf_instance_2019)
storage_config = getattr(gpf_instance_2019.dae_config.storage,
genotype_storage_id)
assert storage_config.storage_type == "filesystem"
gpf_instance_2019.reload()
study = gpf_instance_2019.get_genotype_data(study_id)
assert study is not None
vs = list(study.query_variants())
assert_proper_flexible_short_variants(vs)
def test_import_study_config_arg(
genomes_db_2013,
fixture_dirname,
default_dae_config,
gpf_instance_2013,
temp_dirname,
):
genotype_storage_id = "test_filesystem"
pedigree_filename = fixture_dirname("study_import/comp.ped")
vcf_filename = fixture_dirname("study_import/comp.vcf")
study_config = fixture_dirname("study_import/study_config.conf")
study_id = f"test_comp_vcf_{genotype_storage_id}"
argv = [
pedigree_filename,
"--id",
study_id,
"--skip-reports",
"--vcf-denovo-mode",
"possible_denovo",
"--vcf-omission-mode",
"possible_omission",
"--vcf-files",
vcf_filename,
"--genotype-storage",
genotype_storage_id,
"--study-config",
study_config,
"-F",
"-o",
temp_dirname,
]
main(argv, gpf_instance_2013)
gpf_instance_2013.reload()
study = gpf_instance_2013.get_genotype_data(study_id)
assert study is not None
config = gpf_instance_2013.get_genotype_data_config(study_id)
assert config.name == "asdf"
assert config.description == "Description from study config given to tool"
vs = list(study.query_variants())
assert len(vs) == 30
def test_import_denovo_dae_style_into_genotype_storage(
genotype_storage_id,
storage_type,
genomes_db_2013,
fixture_dirname,
default_dae_config,
gpf_instance_2013,
temp_dirname,
):
pedigree_filename = fixture_dirname("denovo_import/fake_pheno.ped")
denovo_filename = fixture_dirname("denovo_import/variants_DAE_style.tsv")
study_id = f"test_denovo_dae_style_{genotype_storage_id}"
argv = [
pedigree_filename,
"--id",
study_id,
"--skip-reports",
"--denovo-file",
denovo_filename,
"--denovo-location",
"location",
"--denovo-variant",
"variant",
"--denovo-family-id",
"familyId",
"--denovo-best-state",
"bestState",
"--genotype-storage",
genotype_storage_id,
"-o",
temp_dirname,
]
main(argv, gpf_instance_2013)
gpf_instance_2013.reload()
study = gpf_instance_2013.get_genotype_data(study_id)
assert study is not None
vs = list(study.query_variants())
assert len(vs) == 5
def test_import_wild_multivcf_into_genotype_storage(
genotype_storage_id,
storage_type,
genomes_db_2013,
fixture_dirname,
default_dae_config,
gpf_instance_2013,
temp_dirname,
):
vcf_file1 = fixture_dirname("multi_vcf/multivcf_missing1_[vc].vcf.gz")
vcf_file2 = fixture_dirname("multi_vcf/multivcf_missing2_[vc].vcf.gz")
ped_file = fixture_dirname("multi_vcf/multivcf.ped")
study_id = f"test_wile_multivcf_{genotype_storage_id}"
argv = [
ped_file,
"--id",
study_id,
"--skip-reports",
"--vcf-denovo-mode",
"possible_denovo",
"--vcf-omission-mode",
"possible_omission",
"--vcf-files",
vcf_file1,
vcf_file2,
"--vcf-chromosomes",
"chr1;chr2",
"--genotype-storage",
genotype_storage_id,
"-o",
temp_dirname,
]
main(argv, gpf_instance_2013)
gpf_instance_2013.reload()
study = gpf_instance_2013.get_genotype_data(study_id)
assert study is not None
vs = list(study.query_variants())
assert len(vs) == 48
def test_denovo_db_import(
fixture_dirname,
temp_dirname,
genotype_storage_id,
storage_type,
gpf_instance_2013,
):
families_filename = fixture_dirname("backends/denovo-db-person-id.ped")
denovo_filename = fixture_dirname("backends/denovo-db-person-id.tsv")
study_id = f"test_denovo_db_import_{genotype_storage_id}"
argv = [
"--study-id",
study_id,
families_filename,
"-o",
temp_dirname,
"--skip-reports",
"--denovo-chrom",
"Chr",
"--denovo-pos",
"Position",
"--denovo-ref",
"Ref",
"--denovo-alt",
"Alt",
"--denovo-person-id",
"SampleID",
"--denovo-file",
denovo_filename,
"--genotype-storage",
genotype_storage_id,
]
main(argv, gpf_instance_2013)
gpf_instance_2013.reload()
study = gpf_instance_2013.get_genotype_data(study_id)
assert study is not None
vs = list(study.query_variants(inheritance="denovo"))
assert len(vs) == 17
def test_import_transmitted_dae_into_genotype_storage(
genotype_storage_id,
storage_type,
genomes_db_2013,
fixture_dirname,
default_dae_config,
gpf_instance_2013,
temp_dirname,
):
families_filename = fixture_dirname(
"dae_transmitted/transmission.families.txt")
summary_filename = fixture_dirname("dae_transmitted/transmission.txt.gz")
study_id = f"test_dae_transmitted_{genotype_storage_id}"
argv = [
families_filename,
"--ped-file-format",
"simple",
"--id",
study_id,
"--skip-reports",
"--dae-summary-file",
summary_filename,
"--genotype-storage",
genotype_storage_id,
"-o",
temp_dirname,
]
main(argv, gpf_instance_2013)
gpf_instance_2013.reload()
study = gpf_instance_2013.get_genotype_data(study_id)
assert study is not None
vs = list(study.query_variants())
assert len(vs) == 33
def test_add_chrom_prefix_simple(
genotype_storage_id,
storage_type,
genomes_db_2013,
fixture_dirname,
default_dae_config,
gpf_instance_2013,
temp_dirname,
):
pedigree_filename = fixture_dirname("study_import/comp.ped")
vcf_filename = fixture_dirname("study_import/comp.vcf")
denovo_filename = fixture_dirname("study_import/comp.tsv")
study_id = f"test_comp_all_prefix_{genotype_storage_id}"
genotype_storage_id = "test_filesystem"
storage_config = default_dae_config.storage.test_filesystem
assert storage_config.storage_type == "filesystem"
argv = [
pedigree_filename,
"--id",
study_id,
"--skip-reports",
"--vcf-denovo-mode",
"possible_denovo",
"--vcf-omission-mode",
"possible_omission",
"--vcf-files",
vcf_filename,
"--denovo-file",
denovo_filename,
"--denovo-location",
"location",
"--denovo-variant",
"variant",
"--denovo-family-id",
"familyId",
"--denovo-best-state",
"bestState",
"--genotype-storage",
genotype_storage_id,
"-o",
temp_dirname,
"--add-chrom-prefix",
"ala_bala",
]
main(argv, gpf_instance_2013)
gpf_instance_2013.reload()
study = gpf_instance_2013.get_genotype_data(study_id)
assert study is not None
vs = list(study.query_variants())
assert len(vs) == 35
for v in vs:
print(v)
assert v.chromosome.startswith("ala_bala")
for va in v.alleles:
print("\t", va)
assert va.chromosome.startswith("ala_bala")
