def get_es_variants_for_variant_ids(families,
variant_ids,
dataset_type=None,
user=None):
variants = EsSearch(families,
user=user).filter_by_location(variant_ids=variant_ids)
if dataset_type:
variants = variants.update_dataset_type(dataset_type)
return variants.search(num_results=len(variant_ids))
def get_single_es_variant(families,
variant_id,
return_all_queried_families=False):
variants = EsSearch(
families,
return_all_queried_families=return_all_queried_families,
).filter_by_location(variant_ids=[variant_id]).search(num_results=1)
if not variants:
raise Exception('Variant {} not found'.format(variant_id))
return variants[0]
def get_es_variants_for_variant_tuples(families, xpos_ref_alt_tuples):
variant_ids = []
for xpos, ref, alt in xpos_ref_alt_tuples:
chrom, pos = get_chrom_pos(xpos)
if chrom == 'M':
chrom = 'MT'
variant_ids.append('{}-{}-{}-{}'.format(chrom, pos, ref, alt))
variants = EsSearch(families).filter_by_location(
variant_ids=variant_ids).search(num_results=len(xpos_ref_alt_tuples))
return variants
def _parse_variant_items(search_json):
raw_items = search_json.get('rawVariantItems')
if not raw_items:
return None, None, None
invalid_items = []
variant_ids = []
rs_ids = []
for item in raw_items.replace(',', ' ').split():
if item.startswith('rs'):
rs_ids.append(item)
else:
try:
chrom, pos, _, _ = EsSearch.parse_variant_id(item)
get_xpos(chrom, pos)
variant_ids.append(item.lstrip('chr'))
except (KeyError, ValueError):
invalid_items.append(item)
return rs_ids, variant_ids, invalid_items