def obtain_variant_set_for_set(Set): variant_set = variants.VariantSet() variant_set.id = '{}-{}'.format(DATASET_ID, Set) variant_set.name = '{}-{}'.format(SETNAME, Set) variant_set.dataset_id = DATASET_ID variant_set.reference_set_id = '{}-{}'.format(REFERENCE_SET_BASE, Set) brca_meta(variant_set.metadata, DATASET_ID) return variant_set
def get_variant_set(request, variant_set_id): """/variantsets/<set id> method""" if not variant_set_id: return HttpResponseBadRequest(json.dumps( ErrorMessages['variantSetId']), content_type='application/json') dataset, id_ = variant_set_id.split('-') if id_ in SET_IDS and dataset == 'brca': variant_set = variants.VariantSet() variant_set.id = '{}-{}'.format(dataset, id_) variant_set.name = '{}-{}'.format(SETNAME, id_) variant_set.dataset_id = DATASET_ID variant_set.reference_set_id = '{}-{}'.format(REFERENCE_SET_BASE, id_) brca_meta(variant_set.metadata, id_) resp = json_format.MessageToDict(variant_set, True) return JsonResponse(resp) else: return JsonResponse({'Invalid Set Id': variant_set_id}, status=404)
def icgc2pb(input_stream): """ Convert a single icgc somatic variant tsv file into ga4gh variant protobuf ICGC SSM Format: http://docs.icgc.org/submission/guide/icgc-simple-somatic-mutation-format/ """ output_stream = io.BytesIO() for index, icgc in enumerate(csv.DictReader(input_stream, delimiter="\t")): output_stream.write( ga4gh.Variant(id=index, variant_set_id=icgc["icgc_sample_id"], reference_name=icgc["chromosome"], start=icgc["chromosome_start"], end=icgc["chromosome_end"], reference_bases=icgc["mutated_from_allele"], alternate_bases=icgc["mutated_to_allele"])) output_stream.write( ga4gh.VariantSet(id=icgc["icgc_sample_id"], dataset_id=icgc["project_code"])) return output_stream