def get_compound_het_genes(datastore, reference, family, variant_filter=None, quality_filter=None):
"""
Gene-based inheritance; genes with variants that follow compound het inheritance in a family
Note that compound het implies two variants, so we look at all variant pairs
Return is a stream of tuples (gene_name, variant_list)
"""
# only ask for variants that are het in all affected
initial_filter = {}
for indiv_id, individual in family.individuals.items():
if individual.affected_status == 'affected':
initial_filter[indiv_id] = 'ref_alt'
het_variants = get_variants(datastore, family, initial_filter, variant_filter, quality_filter, indivs_to_consider=family.indiv_id_list())
for gene_name, raw_variants in stream_utils.variant_stream_to_gene_stream(het_variants, reference):
variants = search_utils.filter_gene_variants_by_variant_filter(raw_variants, gene_name, variant_filter)
variants_to_return = {}
# don't care about genes w less than 2 variants
if len(variants) < 2:
continue
combos = itertools.combinations(variants, 2)
for combo in combos:
valid = is_family_compound_het_for_combo(combo, family)
if valid:
variants_to_return[combo[0].unique_tuple()] = combo[0]
variants_to_return[combo[1].unique_tuple()] = combo[1]
if len(variants_to_return) > 0:
yield (gene_name, variants_to_return.values())
def get_variants_in_gene(project, gene_id, variant_filter=None, quality_filter=None):
"""
Get all the variants in a gene, but filter out quality_filter genotypes
"""
variant_list = get_project_datastore().get_variants_in_gene(project.project_id, gene_id, variant_filter=variant_filter)
variant_list = search_utils.filter_gene_variants_by_variant_filter(variant_list, gene_id, variant_filter)
return variant_list
def get_knockouts_in_gene(project, gene_id, quality_filter=None):
"""
Get all the variants in a gene, but filter out quality_filter genotypes
"""
indiv_id_list = [i.indiv_id for i in project.get_individuals()]
# filter out variants > 0.01 AF in any of the reference populations
reference_populations = mall.get_annotator().reference_population_slugs
variant_filter = get_default_variant_filter('moderate_impact',
reference_populations)
variant_list = get_project_datastore(
project.project_id).get_project_variants_in_gene(
project.project_id,
gene_id,
variant_filter=variant_filter,
)
variant_list = search_utils.filter_gene_variants_by_variant_filter(
variant_list, gene_id, variant_filter)
variation = CohortGeneVariation(
get_reference(),
gene_id,
variant_list,
indiv_id_list,
quality_filter={},
)
knockouts = get_individuals_with_inheritance('recessive', variation,
indiv_id_list)
return knockouts, variation
def get_variants_in_gene(family_group,
gene_id,
variant_filter=None,
quality_filter=None):
"""
"""
variants_by_family = []
for family in family_group.get_families():
variant_list = list(
get_mall(
family.project.project_id).variant_store.get_variants_in_gene(
family.project.project_id,
family.family_id,
gene_id,
variant_filter=variant_filter))
variant_list = search_utils.filter_gene_variants_by_variant_filter(
variant_list, gene_id, variant_filter)
add_extra_info_to_variants_family(get_reference(), family,
variant_list)
variants_by_family.append({
'variants': [v.toJSON() for v in variant_list],
'family_id':
family.family_id,
'project_id':
family.project.project_id,
'family_name':
str(family),
})
return variants_by_family
def get_compound_het_genes(datastore, reference, family, variant_filter=None, quality_filter=None):
"""
Gene-based inheritance; genes with variants that follow compound het inheritance in a family
Note that compound het implies two variants, so we look at all variant pairs
Return is a stream of tuples (gene_name, variant_list)
"""
# only ask for variants that are het in all affected
initial_filter = {}
for indiv_id, individual in family.individuals.items():
if individual.affected_status == 'affected':
initial_filter[indiv_id] = 'ref_alt'
het_variants = get_variants(datastore, family, initial_filter, variant_filter, quality_filter, indivs_to_consider=family.indiv_id_list())
for gene_name, raw_variants in stream_utils.variant_stream_to_gene_stream(het_variants, reference):
variants = search_utils.filter_gene_variants_by_variant_filter(raw_variants, gene_name, variant_filter)
variants_to_return = {}
# don't care about genes w less than 2 variants
if len(variants) < 2:
continue
combos = itertools.combinations(variants, 2)
for combo in combos:
valid = is_family_compound_het_for_combo(combo, family)
if valid:
variants_to_return[combo[0].unique_tuple()] = combo[0]
variants_to_return[combo[1].unique_tuple()] = combo[1]
if len(variants_to_return) > 0:
yield (gene_name, variants_to_return.values())
def get_variants_in_gene(project, gene_id, variant_filter=None, quality_filter=None):
"""
Get all the variants in a gene, but filter out quality_filter genotypes
"""
variant_list = get_project_datastore(project).get_project_variants_in_gene(project.project_id, gene_id, variant_filter=variant_filter)
variant_list = search_utils.filter_gene_variants_by_variant_filter(variant_list, gene_id, variant_filter)
return variant_list
def get_genes_with_inheritance(datastore, reference, cohort, inheritance_mode, variant_filter=None, quality_filter=None):
"""
"""
for gene_id, raw_variant_list in get_genes(datastore, reference, cohort, variant_filter):
variant_list = search_utils.filter_gene_variants_by_variant_filter(raw_variant_list, gene_id, variant_filter)
gene_variation = CohortGeneVariation(reference, gene_id, variant_list, cohort.indiv_id_list(), quality_filter=quality_filter)
indivs_with_inheritance = get_individuals_with_inheritance(inheritance_mode, gene_variation, cohort.indiv_id_list())
if len(indivs_with_inheritance) > 0:
yield gene_id, indivs_with_inheritance, gene_variation
def get_genes_with_inheritance(datastore, reference, cohort, inheritance_mode, variant_filter=None, quality_filter=None):
"""
"""
for gene_id, raw_variant_list in get_genes(datastore, reference, cohort, variant_filter):
variant_list = search_utils.filter_gene_variants_by_variant_filter(raw_variant_list, gene_id, variant_filter)
gene_variation = CohortGeneVariation(reference, gene_id, variant_list, cohort.indiv_id_list(), quality_filter=quality_filter)
indivs_with_inheritance = get_individuals_with_inheritance(inheritance_mode, gene_variation, cohort.indiv_id_list())
if len(indivs_with_inheritance) > 0:
yield gene_id, indivs_with_inheritance, gene_variation
def get_individuals_with_inheritance_in_gene(datastore, reference, cohort, inheritance_mode, gene_id, variant_filter=None, quality_filter=None):
variant_list = list(datastore.get_variants_in_gene(
cohort.project_id,
cohort.cohort_id,
gene_id,
variant_filter=variant_filter,
))
variant_list = search_utils.filter_gene_variants_by_variant_filter(variant_list, gene_id, variant_filter)
gene_variation = CohortGeneVariation(reference, gene_id, variant_list, cohort.indiv_id_list(), quality_filter=quality_filter)
indivs_with_inheritance = get_individuals_with_inheritance(inheritance_mode, gene_variation, cohort.indiv_id_list())
return indivs_with_inheritance, gene_variation
def get_individuals_with_inheritance_in_gene(datastore, reference, cohort, inheritance_mode, gene_id, variant_filter=None, quality_filter=None):
variant_list = list(datastore.get_variants_in_gene(
cohort.project_id,
cohort.cohort_id,
gene_id,
variant_filter=variant_filter,
))
variant_list = search_utils.filter_gene_variants_by_variant_filter(variant_list, gene_id, variant_filter)
gene_variation = CohortGeneVariation(reference, gene_id, variant_list, cohort.indiv_id_list(), quality_filter=quality_filter)
indivs_with_inheritance = get_individuals_with_inheritance(inheritance_mode, gene_variation, cohort.indiv_id_list())
return indivs_with_inheritance, gene_variation
def get_knockouts_in_gene(project, gene_id, gene_variants):
"""
Get all the variants in a gene, but filter out quality_filter genotypes
"""
indiv_id_list = [i.indiv_id for i in project.get_individuals()]
# filter out variants > 0.01 AF in any of the reference populations
reference_populations = mall.get_annotator().reference_population_slugs
variant_filter = get_default_variant_filter('moderate_impact', reference_populations)
variant_list = search_utils.filter_gene_variants_by_variant_filter(gene_variants, gene_id, variant_filter)
variation = CohortGeneVariation(
get_reference(),
gene_id,
variant_list,
indiv_id_list,
quality_filter={},
)
knockouts = get_individuals_with_inheritance('recessive', variation, indiv_id_list)
return knockouts, variation
def get_knockouts_in_gene(project, gene_id, quality_filter=None):
"""
Get all the variants in a gene, but filter out quality_filter genotypes
"""
indiv_id_list = [i.indiv_id for i in project.get_individuals()]
variant_filter = get_default_variant_filter('high_impact')
variant_list = get_project_datastore().get_variants_in_gene(
project.project_id,
gene_id,
variant_filter=variant_filter,
)
variant_list = search_utils.filter_gene_variants_by_variant_filter(variant_list, gene_id, variant_filter)
variation = CohortGeneVariation(
get_reference(),
gene_id,
variant_list,
indiv_id_list,
quality_filter={},
)
knockouts = get_individuals_with_inheritance('recessive', variation, indiv_id_list)
return knockouts, variation
def get_variants_in_gene(family_group, gene_id, variant_filter=None, quality_filter=None):
"""
"""
variants_by_family = []
for family in family_group.get_families():
variant_list = list(get_mall(family.project.project_id).variant_store.get_variants_in_gene(
family.project.project_id,
family.family_id,
gene_id,
variant_filter=variant_filter
))
variant_list = search_utils.filter_gene_variants_by_variant_filter(variant_list, gene_id, variant_filter)
add_extra_info_to_variants_family(get_reference(), family, variant_list)
variants_by_family.append({
'variants': [v.toJSON() for v in variant_list],
'family_id': family.family_id,
'project_id': family.project.project_id,
'family_name': str(family),
})
return variants_by_family
def get_knockouts_in_gene(project, gene_id, quality_filter=None):
"""
Get all the variants in a gene, but filter out quality_filter genotypes
"""
indiv_id_list = [i.indiv_id for i in project.get_individuals()]
variant_filter = get_default_variant_filter('high_impact')
variant_list = get_project_datastore(
project.project_id).get_project_variants_in_gene(
project.project_id,
gene_id,
variant_filter=variant_filter,
)
variant_list = search_utils.filter_gene_variants_by_variant_filter(
variant_list, gene_id, variant_filter)
variation = CohortGeneVariation(
get_reference(),
gene_id,
variant_list,
indiv_id_list,
quality_filter={},
)
knockouts = get_individuals_with_inheritance('recessive', variation,
indiv_id_list)
return knockouts, variation
