"gs://seqr-reference-data/GRCh38/gnomad/coverage/gnomad.chr5.cov.liftover.GRCh38.txt.gz", "gs://seqr-reference-data/GRCh38/gnomad/coverage/gnomad.chr6.cov.liftover.GRCh38.txt.gz", "gs://seqr-reference-data/GRCh38/gnomad/coverage/gnomad.chr7.cov.liftover.GRCh38.txt.gz", "gs://seqr-reference-data/GRCh38/gnomad/coverage/gnomad.chr8.cov.liftover.GRCh38.txt.gz", "gs://seqr-reference-data/GRCh38/gnomad/coverage/gnomad.chr9.cov.liftover.GRCh38.txt.gz", "gs://seqr-reference-data/GRCh38/gnomad/coverage/gnomad.chrX.cov.liftover.GRCh38.txt.gz", ], "output_path": "gs://%(output_bucket)s/GRCh38/gnomad/genomes.coverage.vds" % args.__dict__, }, } field_types = { '#chrom': TString(), 'pos': TInt(), 'mean': TDouble(), 'median': TDouble(), '1': TDouble(), '5': TDouble(), '10': TDouble(), '15': TDouble(), '20': TDouble(), '25': TDouble(), '30': TDouble(), '50': TDouble(), '100': TDouble(), } for label, data_paths in COVERAGE_TSV_PATHS.items():
hc = hail.HailContext(log="/tmp/hail.log") gene_results_url = "gs://epi-browser/2018-11-07_epi25-exome-browser-gene-results-table-reduced.csv" kt = hc.import_table(gene_results_url, delimiter=",", missing="NA", quote='"', types={ 'gene_name': TString(), 'description': TString(), 'gene_id': TString(), 'xcase_lof': TInt(), 'xctrl_lof': TInt(), 'pval_lof': TDouble(), 'xcase_mpc': TInt(), 'xctrl_mpc': TInt(), 'pval_mpc': TDouble(), 'xcase_infrIndel': TInt(), 'xctrl_infrIndel': TInt(), 'pval_infrIndel': TDouble(), 'pval_meta': TDouble(), 'analysis_group': TString(), }) es = ElasticsearchClient(args.host, args.port) es.export_kt_to_elasticsearch( kt, index_name="epi_exome_gene_results_181107",
type=int) p.add_argument("-s", "--num-shards", help="Number of shards", default=1, type=int) # parse args args = p.parse_args() hc = hail.HailContext(log="/hail.log") #, branching_factor=1) FILE_PATH = 'gs://gnomad-browser/datasets/gtex_tissues_by_transcript_all_171012.csv' types = { 'adiposeSubcutaneous': TDouble(), 'adiposeVisceralOmentum': TDouble(), 'adrenalGland': TDouble(), 'arteryAorta': TDouble(), 'arteryCoronary': TDouble(), 'arteryTibial': TDouble(), 'bladder': TDouble(), 'brainAmygdala': TDouble(), 'brainAnteriorcingulatecortexBa24': TDouble(), 'brainCaudateBasalganglia': TDouble(), 'brainCerebellarhemisphere': TDouble(), 'brainCerebellum': TDouble(), 'brainCortex': TDouble(), 'brainFrontalcortexBa9': TDouble(), 'brainHippocampus': TDouble(), 'brainHypothalamus': TDouble(),