def _get_saved_variants(variants, families, include_discovery_tags=False):
variants = _flatten_variants(variants)
prefetch_related_objects(families, 'project')
hg37_family_guids = {family.guid for family in families if family.project.genome_version == GENOME_VERSION_GRCh37}
variant_q = Q()
variants_by_id = {}
for variant in variants:
variants_by_id[get_variant_key(**variant)] = variant
variant_q |= Q(variant_id=variant['variantId'], family__guid__in=variant['familyGuids'])
if variant['liftedOverGenomeVersion'] == GENOME_VERSION_GRCh37 and hg37_family_guids:
variant_hg37_families = [family_guid for family_guid in variant['familyGuids'] if family_guid in hg37_family_guids]
if variant_hg37_families:
lifted_xpos = get_xpos(variant['liftedOverChrom'], variant['liftedOverPos'])
variant_q |= Q(xpos=lifted_xpos, ref=variant['ref'], alt=variant['alt'], family__guid__in=variant_hg37_families)
variants_by_id[get_variant_key(
xpos=lifted_xpos, ref=variant['ref'], alt=variant['alt'], genomeVersion=variant['liftedOverGenomeVersion']
)] = variant
saved_variants = SavedVariant.objects.filter(variant_q)
json = get_json_for_saved_variants_with_tags(saved_variants, add_details=True)
discovery_tags = {}
if include_discovery_tags:
discovery_tags, discovery_response = get_json_for_discovery_tags(variants)
json.update(discovery_response)
variants_to_saved_variants = {}
for saved_variant in json['savedVariantsByGuid'].values():
family_guids = saved_variant['familyGuids']
searched_variant = variants_by_id.get(get_variant_key(**saved_variant))
if not searched_variant:
# This can occur when an hg38 family has a saved variant that did not successfully lift from hg37
continue
saved_variant.update(searched_variant)
# For saved variants only use family it was saved for, not all families in search
saved_variant['familyGuids'] = family_guids
json['savedVariantsByGuid'][saved_variant['variantGuid']] = saved_variant
if searched_variant['variantId'] not in variants_to_saved_variants:
variants_to_saved_variants[searched_variant['variantId']] = {}
for family_guid in family_guids:
variants_to_saved_variants[searched_variant['variantId']][family_guid] = saved_variant['variantGuid']
for variant_id, tags in discovery_tags.items():
searched_variant = variants_by_id.get(variant_id)
if searched_variant:
if not searched_variant.get('discoveryTags'):
searched_variant['discoveryTags'] = []
searched_variant['discoveryTags'] += [
tag for tag in tags if tag['savedVariant']['familyGuid'] not in searched_variant['familyGuids']]
return json, variants_to_saved_variants
def _add_discovery_tags(variants, discovery_tags):
for variant in variants:
tags = discovery_tags.get(get_variant_key(**variant))
if tags:
if not variant.get('discoveryTags'):
variant['discoveryTags'] = []
variant['discoveryTags'] += tags
def _add_discovery_tags(variants, discovery_tags):
for variant in variants:
tags = discovery_tags.get(get_variant_key(**variant))
if tags:
if not variant.get('discoveryTags'):
variant['discoveryTags'] = []
variant['discoveryTags'] += [tag for tag in tags if tag['savedVariant']['familyGuid'] not in variant['familyGuids']]
def get_json_for_discovery_tags(variants):
from seqr.views.utils.variant_utils import get_variant_key
response = {}
discovery_tags = defaultdict(list)
tag_models = VariantTag.objects.filter(
variant_tag_type__category='CMG Discovery Tags',
saved_variants__variant_id__in={
variant['variantId']
for variant in variants
},
saved_variants__family__project__projectcategory__name=
ANALYST_PROJECT_CATEGORY,
)
if tag_models:
discovery_tag_json = get_json_for_variant_tags(tag_models,
add_variant_guids=False)
tag_id_map = {tag.guid: tag.id for tag in tag_models}
variant_tag_id_map = defaultdict(list)
variant_ids = set()
for tag_mapping in VariantTag.saved_variants.through.objects.filter(
varianttag_id__in=tag_id_map.values()):
variant_tag_id_map[tag_mapping.varianttag_id].append(
tag_mapping.savedvariant_id)
variant_ids.add(tag_mapping.savedvariant_id)
saved_variants_by_id = {
var.id: var
for var in SavedVariant.objects.filter(id__in=variant_ids).only(
'guid', 'ref', 'alt', 'xpos', 'family_id').prefetch_related(
'family', 'family__project')
}
existing_families = set()
for variant in variants:
existing_families.update(variant['familyGuids'])
families = set()
for tag in discovery_tag_json:
for variant_id in variant_tag_id_map[tag_id_map[tag['tagGuid']]]:
variant = saved_variants_by_id[variant_id]
if variant.family.guid not in existing_families:
families.add(variant.family)
tag_json = {
'savedVariant': {
'variantGuid': variant.guid,
'familyGuid': variant.family.guid,
'projectGuid': variant.family.project.guid,
}
}
tag_json.update(tag)
variant_key = get_variant_key(
genomeVersion=variant.family.project.genome_version,
xpos=variant.xpos,
ref=variant.ref,
alt=variant.alt,
)
discovery_tags[variant_key].append(tag_json)
response['familiesByGuid'] = {
f['familyGuid']: f
for f in _get_json_for_families(list(families))
}
return discovery_tags, response
def get_json_for_saved_variants_with_tags(saved_variants,
include_missing_variants=False,
discovery_tags_query=None,
**kwargs):
variants_by_guid = {
variant['variantGuid']: dict(tagGuids=[],
functionalDataGuids=[],
noteGuids=[],
**variant)
for variant in get_json_for_saved_variants(saved_variants, **kwargs)
}
missing_ids = set()
saved_variant_id_map = {var.id: var.guid for var in saved_variants}
variant_tag_id_map = defaultdict(list)
for tag_mapping in VariantTag.saved_variants.through.objects.filter(
savedvariant_id__in=saved_variant_id_map.keys()):
variant_tag_id_map[tag_mapping.varianttag_id].append(
tag_mapping.savedvariant_id)
tag_models = VariantTag.objects.filter(id__in=variant_tag_id_map.keys())
tag_id_map = {tag.guid: tag.id for tag in tag_models}
tags = get_json_for_variant_tags(tag_models, add_variant_guids=False)
for tag in tags:
tag_guid = tag['tagGuid']
tag['variantGuids'] = []
variant_ids = variant_tag_id_map[tag_id_map[tag_guid]]
for variant_id in variant_ids:
variant_guid = saved_variant_id_map.get(variant_id)
if variant_guid:
variants_by_guid[variant_guid]['tagGuids'].append(
tag['tagGuid'])
tag['variantGuids'].append(variant_guid)
else:
missing_ids.add(variant_id)
variant_functional_id_map = defaultdict(list)
for functional_mapping in VariantFunctionalData.saved_variants.through.objects.filter(
savedvariant_id__in=saved_variant_id_map.keys()):
variant_functional_id_map[
functional_mapping.variantfunctionaldata_id].append(
functional_mapping.savedvariant_id)
functional_models = VariantFunctionalData.objects.filter(
id__in=variant_functional_id_map.keys())
functional_id_map = {tag.guid: tag.id for tag in functional_models}
functional_data = get_json_for_variant_functional_data_tags(
functional_models, add_variant_guids=False)
for tag in functional_data:
tag_guid = tag['tagGuid']
tag['variantGuids'] = []
variant_ids = variant_functional_id_map[functional_id_map[tag_guid]]
for variant_id in variant_ids:
variant_guid = saved_variant_id_map.get(variant_id)
if variant_guid:
variants_by_guid[variant_guid]['functionalDataGuids'].append(
tag['tagGuid'])
tag['variantGuids'].append(variant_guid)
else:
missing_ids.add(variant_id)
variant_note_id_map = defaultdict(list)
for note_mapping in VariantNote.saved_variants.through.objects.filter(
savedvariant_id__in=saved_variant_id_map.keys()):
variant_note_id_map[note_mapping.variantnote_id].append(
note_mapping.savedvariant_id)
note_models = VariantNote.objects.filter(id__in=variant_note_id_map.keys())
note_id_map = {note.guid: note.id for note in note_models}
notes = get_json_for_variant_notes(note_models, add_variant_guids=False)
for note in notes:
note_guid = note['noteGuid']
note['variantGuids'] = []
variant_ids = variant_note_id_map[note_id_map[note_guid]]
for variant_id in variant_ids:
variant_guid = saved_variant_id_map.get(variant_id)
if variant_guid:
variants_by_guid[variant_guid]['noteGuids'].append(
note['noteGuid'])
note['variantGuids'].append(variant_guid)
else:
missing_ids.add(variant_id)
if include_missing_variants and missing_ids:
variants_by_guid.update({
variant['variantGuid']: dict(tagGuids=[],
functionalDataGuids=[],
noteGuids=[],
**variant)
for variant in get_json_for_saved_variants(
SavedVariant.objects.filter(id__in=missing_ids), **kwargs)
})
response = {
'variantTagsByGuid': {tag['tagGuid']: tag
for tag in tags},
'variantNotesByGuid': {note['noteGuid']: note
for note in notes},
'variantFunctionalDataByGuid':
{tag['tagGuid']: tag
for tag in functional_data},
'savedVariantsByGuid': variants_by_guid,
}
if discovery_tags_query:
from seqr.views.utils.variant_utils import get_variant_key
discovery_saved_variant_by_guid = {
var.guid: var
for var in SavedVariant.objects.filter(discovery_tags_query).
prefetch_related('family', 'family__project')
}
discovery_tags = get_json_for_variant_tags(
VariantTag.objects.filter(
variant_tag_type__category='CMG Discovery Tags',
saved_variants__in=discovery_saved_variant_by_guid.values()))
if discovery_tags:
families = set()
response['discoveryTags'] = defaultdict(list)
for tag in discovery_tags:
for variant_guid in tag.pop('variantGuids'):
variant = discovery_saved_variant_by_guid.get(variant_guid)
if variant:
families.add(variant.family)
tag_json = {
'savedVariant': {
'variantGuid': variant.guid,
'familyGuid': variant.family.guid,
'projectGuid': variant.family.project.guid,
}
}
tag_json.update(tag)
variant_key = get_variant_key(
genomeVersion=variant.family.project.
genome_version,
xpos=variant.xpos,
ref=variant.ref,
alt=variant.alt,
)
response['discoveryTags'][variant_key].append(tag_json)
response['familiesByGuid'] = {
f['familyGuid']: f
for f in _get_json_for_families(list(families))
}
return response