"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(),