def get_variants_with_inheritance_mode(mall,
family,
inheritance_mode,
variant_filter=None,
quality_filter=None,
user=None):
"""
Get variants in a family with inheritance_mode, using the functions in VARIANT_INHERITANCE_FUNCTIONS
"""
if inheritance_modes.INHERITANCE_DEFAULTS_MAP[inheritance_mode][
'datatype'] == 'variants':
for variant in INHERITANCE_FUNCTIONS[inheritance_mode](
mall.variant_store,
mall.reference,
family,
variant_filter=variant_filter,
quality_filter=quality_filter,
user=user):
yield variant
else:
for variant in stream_utils.gene_stream_to_variant_stream(
INHERITANCE_FUNCTIONS[inheritance_mode](
mall.variant_store,
mall.reference,
family,
variant_filter=variant_filter,
quality_filter=quality_filter,
user=user), mall.reference):
yield variant
def calculate_mendelian_variant_search(search_spec, xfamily):
variants = None
if search_spec.search_mode == 'standard_inheritance':
variants = list(get_variants_with_inheritance_mode(
get_mall(),
xfamily,
search_spec.inheritance_mode,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.genotype_quality_filter,
))
elif search_spec.search_mode == 'custom_inheritance':
variants = list(get_variants_family(
get_datastore(),
xfamily,
genotype_filter=search_spec.genotype_inheritance_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.genotype_quality_filter,
))
elif search_spec.search_mode == 'gene_burden':
gene_stream = get_genes_family(
get_datastore(),
get_reference(),
xfamily,
burden_filter=search_spec.gene_burden_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.genotype_quality_filter,
)
variants = list(stream_utils.gene_stream_to_variant_stream(gene_stream, get_reference()))
elif search_spec.search_mode == 'allele_count':
variants = list(get_variants_allele_count(
get_datastore(),
xfamily,
search_spec.allele_count_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.genotype_quality_filter,
))
elif search_spec.search_mode == 'all_variants':
variants = list(get_variants_family(
get_datastore(),
xfamily,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.genotype_quality_filter,
))
return variants
def get_variants_with_inheritance_mode(mall, family, inheritance_mode, variant_filter=None, quality_filter=None):
"""
Get variants in a family with inheritance_mode, using the functions in VARIANT_INHERITANCE_FUNCTIONS
"""
if inheritance_modes.INHERITANCE_DEFAULTS_MAP[inheritance_mode]['datatype'] == 'variants':
for variant in INHERITANCE_FUNCTIONS[inheritance_mode](mall.variant_store, mall.reference, family, variant_filter, quality_filter):
yield variant
else:
for variant in stream_utils.gene_stream_to_variant_stream(INHERITANCE_FUNCTIONS[inheritance_mode](mall.variant_store, mall.reference, family, variant_filter, quality_filter), mall.reference):
yield variant
def calculate_mendelian_variant_search(search_spec, xfamily):
sys.stderr.write(" mendelian_variant_search for %s - search mode: %s %s\n" % (xfamily.project_id, search_spec.search_mode, search_spec.__dict__))
variants = None
if search_spec.search_mode == 'standard_inheritance':
variants = list(get_variants_with_inheritance_mode(
get_mall(xfamily.project_id),
xfamily,
search_spec.inheritance_mode,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
))
elif search_spec.search_mode == 'custom_inheritance':
variants = list(get_variants_family(
get_datastore(xfamily.project_id),
xfamily,
genotype_filter=search_spec.genotype_inheritance_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
))
elif search_spec.search_mode == 'gene_burden':
gene_stream = get_genes_family(
get_datastore(xfamily.project_id),
get_reference(),
xfamily,
burden_filter=search_spec.gene_burden_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
)
variants = list(stream_utils.gene_stream_to_variant_stream(gene_stream, get_reference()))
elif search_spec.search_mode == 'allele_count':
variants = list(get_variants_allele_count(
get_datastore(xfamily.project_id),
xfamily,
search_spec.allele_count_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
))
elif search_spec.search_mode == 'all_variants':
variants = list(get_variants_family(
get_datastore(xfamily.project_id),
xfamily,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
indivs_to_consider=xfamily.indiv_id_list(),
))
return variants
def calculate_mendelian_variant_search(search_spec, family, user=None):
xfamily = family.xfamily()
project = family.project
variants = None
if search_spec.search_mode == 'standard_inheritance':
variants = list(get_variants_with_inheritance_mode(
get_mall(project),
xfamily,
search_spec.inheritance_mode,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
user=user,
))
elif search_spec.search_mode == 'custom_inheritance':
variants = list(get_variants_family(
get_datastore(project),
xfamily,
genotype_filter=search_spec.genotype_inheritance_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
user=user,
))
elif search_spec.search_mode == 'gene_burden':
gene_stream = get_genes_family(
get_datastore(project),
get_reference(),
xfamily,
burden_filter=search_spec.gene_burden_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
user=user,
)
variants = list(stream_utils.gene_stream_to_variant_stream(gene_stream, get_reference()))
elif search_spec.search_mode == 'allele_count':
variants = list(get_variants_allele_count(
get_datastore(project),
xfamily,
search_spec.allele_count_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
user=user,
))
elif search_spec.search_mode == 'all_variants':
variants = list(get_variants_family(
get_datastore(project),
xfamily,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
indivs_to_consider=xfamily.indiv_id_list(),
user=user,
))
for variant in variants:
variant.set_extra('family_id', family.family_id)
return variants
def calculate_mendelian_variant_search(search_spec, xfamily):
sys.stderr.write(" cohort_variant_search - inheritance_mode: %s" %
search_spec.inheritance_mode)
variants = None
if search_spec.search_mode == 'standard_inheritance':
variants = list(
get_variants_with_inheritance_mode(
get_mall(xfamily.project_id),
xfamily,
search_spec.inheritance_mode,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.genotype_quality_filter,
))
elif search_spec.search_mode == 'custom_inheritance':
variants = list(
get_variants_family(
get_datastore(xfamily.project_id),
xfamily,
genotype_filter=search_spec.genotype_inheritance_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.genotype_quality_filter,
))
elif search_spec.search_mode == 'gene_burden':
gene_stream = get_genes_family(
get_datastore(xfamily.project_id),
get_reference(),
xfamily,
burden_filter=search_spec.gene_burden_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.genotype_quality_filter,
)
variants = list(
stream_utils.gene_stream_to_variant_stream(gene_stream,
get_reference()))
elif search_spec.search_mode == 'allele_count':
variants = list(
get_variants_allele_count(
get_datastore(xfamily.project_id),
xfamily,
search_spec.allele_count_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.genotype_quality_filter,
))
elif search_spec.search_mode == 'all_variants':
variants = list(
get_variants_family(
get_datastore(xfamily.project_id),
xfamily,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.genotype_quality_filter,
))
return variants
def calculate_mendelian_variant_search(search_spec, family, user=None):
xfamily = family.xfamily()
project = family.project
variants = None
if search_spec.search_mode == 'standard_inheritance':
variants = list(
get_variants_with_inheritance_mode(
get_mall(project),
xfamily,
search_spec.inheritance_mode,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
user=user,
))
elif search_spec.search_mode == 'custom_inheritance':
variants = list(
get_variants_family(
get_datastore(project),
xfamily,
genotype_filter=search_spec.genotype_inheritance_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
user=user,
))
elif search_spec.search_mode == 'gene_burden':
gene_stream = get_genes_family(
get_datastore(project),
get_reference(),
xfamily,
burden_filter=search_spec.gene_burden_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
user=user,
)
variants = list(
stream_utils.gene_stream_to_variant_stream(gene_stream,
get_reference()))
elif search_spec.search_mode == 'allele_count':
variants = list(
get_variants_allele_count(
get_datastore(project),
xfamily,
search_spec.allele_count_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
user=user,
))
elif search_spec.search_mode == 'all_variants':
variants = list(
get_variants_family(
get_datastore(project),
xfamily,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
indivs_to_consider=xfamily.indiv_id_list(),
user=user,
))
for variant in variants:
variant.set_extra('family_id', family.family_id)
return variants
def calculate_mendelian_variant_search(search_spec, xfamily):
sys.stderr.write((
"mendelian_variant_search for %s - search mode: %s \n"
"variant_filter: %s \ninheritance_mode: %s \nallele_count_filter: %s \nquality_filter: %s \ngenotype_inheritance_filter: %s \n"
) % (xfamily.project_id, search_spec.search_mode,
search_spec.variant_filter.toJSON() if search_spec.variant_filter else
'', search_spec.inheritance_mode, search_spec.allele_count_filter,
search_spec.quality_filter, search_spec.genotype_inheritance_filter))
variants = None
if search_spec.search_mode == 'standard_inheritance':
variants = list(
get_variants_with_inheritance_mode(
get_mall(xfamily.project_id),
xfamily,
search_spec.inheritance_mode,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
))
elif search_spec.search_mode == 'custom_inheritance':
variants = list(
get_variants_family(
get_datastore(xfamily.project_id),
xfamily,
genotype_filter=search_spec.genotype_inheritance_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
))
elif search_spec.search_mode == 'gene_burden':
gene_stream = get_genes_family(
get_datastore(xfamily.project_id),
get_reference(),
xfamily,
burden_filter=search_spec.gene_burden_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
)
variants = list(
stream_utils.gene_stream_to_variant_stream(gene_stream,
get_reference()))
elif search_spec.search_mode == 'allele_count':
variants = list(
get_variants_allele_count(
get_datastore(xfamily.project_id),
xfamily,
search_spec.allele_count_filter,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
))
elif search_spec.search_mode == 'all_variants':
variants = list(
get_variants_family(
get_datastore(xfamily.project_id),
xfamily,
variant_filter=search_spec.variant_filter,
quality_filter=search_spec.quality_filter,
indivs_to_consider=xfamily.indiv_id_list(),
))
return variants
