def load_singlecore(args):
# create a new gemini loader and populate
# the gemini db and files from the VCF
gemini_loader = GeminiLoader(args)
gemini_loader.store_resources()
gemini_loader.store_version()
gemini_loader.populate_from_vcf()
if not args.skip_gene_tables and not args.test_mode:
gemini_loader.update_gene_table()
if not args.test_mode:
gemini_loader.build_indices_and_disconnect()
if not args.no_genotypes and not args.no_load_genotypes:
gemini_loader.store_sample_gt_counts()
gemini_annotate.add_extras(args.db, [args.db])
def load_singlecore(args):
# create a new gemini loader and populate
# the gemini db and files from the VCF
gemini_loader = GeminiLoader(args)
gemini_loader.store_resources()
gemini_loader.store_version()
gemini_loader.populate_from_vcf()
if not args.skip_gene_tables and not args.test_mode:
gemini_loader.update_gene_table()
if not args.test_mode:
gemini_loader.build_indices_and_disconnect()
if not args.no_genotypes and not args.no_load_genotypes:
gemini_loader.store_sample_gt_counts()
gemini_annotate.add_extras(args.db, [args.db])
def load_ipython(args):
grabix_file = bgzip(args.vcf)
with cluster_view(*get_ipython_args(args)) as view:
chunks = load_chunks_ipython(grabix_file, args, view)
merge_chunks_ipython(chunks, args.db, view)
gemini_annotate.add_extras(args.db, chunks)
def load_multicore(args):
grabix_file = bgzip(args.vcf)
chunks = load_chunks_multicore(grabix_file, args)
merge_chunks_multicore(chunks, args.db)
gemini_annotate.add_extras(args.db, chunks)
def load_ipython(args):
grabix_file = bgzip(args.vcf)
with cluster_view(*get_ipython_args(args)) as view:
chunks = load_chunks_ipython(grabix_file, args, view)
merge_chunks_ipython(chunks, args.db, view)
gemini_annotate.add_extras(args.db, chunks)
def load_multicore(args):
grabix_file = bgzip(args.vcf)
chunks = load_chunks_multicore(grabix_file, args)
merge_chunks_multicore(chunks, args.db)
gemini_annotate.add_extras(args.db, chunks)
def load_multicore(args):
grabix_file = bgzip(args.vcf)
chunks = load_chunks_multicore(grabix_file, args)
merge_chunks_multicore(chunks, args)
gemini_annotate.add_extras(args.db, chunks, region_only=False, tempdir=args.tempdir)
