def load_singlecore(args):
# create a new gemini loader and populate
# the gemini db and files from the VCF
l = GeminiLoader(args)
l.populate_from_vcf()
if not args.no_genotypes and not args.no_load_genotypes:
l.store_sample_gt_counts()
return l
def load_singlecore(args):
# create a new gemini loader and populate
# the gemini db and files from the VCF
l = GeminiLoader(args)
l.populate_from_vcf()
if not args.no_genotypes and not args.no_load_genotypes:
l.store_sample_gt_counts()
return l
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()
gemini_loader.build_indices_and_disconnect()
if not args.no_genotypes and not args.no_load_genotypes:
gemini_loader.store_sample_gt_counts()
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()
gemini_loader.build_indices_and_disconnect()
if not args.no_genotypes and not args.no_load_genotypes:
gemini_loader.store_sample_gt_counts()
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_singlecore(args):
# create a new geminicassandra loader and populate
# the geminicassandra db and files from the VCF
gemini_loader = GeminiLoader(args)
gemini_loader.connect_to_db()
if not args.no_genotypes and not args.no_load_genotypes:
gemini_loader._init_sample_gt_counts()
gemini_loader.populate_from_vcf()
'''if not args.skip_gene_tables and not args.test_mode:
gemini_loader.update_gene_table()'''
if not args.no_genotypes and not args.no_load_genotypes:
gemini_loader.store_sample_gt_counts()
if not args.test_mode:
gemini_loader.disconnect()
def load_singlecore(args):
# create a new geminicassandra loader and populate
# the geminicassandra db and files from the VCF
gemini_loader = GeminiLoader(args)
gemini_loader.connect_to_db()
if not args.no_genotypes and not args.no_load_genotypes:
gemini_loader._init_sample_gt_counts()
gemini_loader.populate_from_vcf()
'''if not args.skip_gene_tables and not args.test_mode:
gemini_loader.update_gene_table()'''
if not args.no_genotypes and not args.no_load_genotypes:
gemini_loader.store_sample_gt_counts()
if not args.test_mode:
gemini_loader.disconnect()
