def finish(args, loader=None):
"""
all things that are performed by single core, multi, ipython
should be done here
"""
if loader is None:
loader = GeminiLoader(args, prepare_db=False)
print "storing version, header, etc."
loader.store_resources()
loader.store_version()
loader.store_vcf_header()
if not args.skip_gene_tables:
print "storing gene-detailed"
loader._get_gene_detailed()
print "storing gene-summary"
loader._get_gene_summary()
if not args.test_mode:
print "updating gene-table"
loader.update_gene_table()
if not args.test_mode:
print "building indices"
loader.build_indices_and_disconnect()
else:
import database
database.close_and_commit(loader.c)
def finish(args, loader=None):
"""
all things that are performed by single core, multi, ipython
should be done here
"""
if loader is None:
loader = GeminiLoader(args, prepare_db=False)
print "storing version, header, etc."
loader.store_resources()
loader.store_version()
loader.store_vcf_header()
if not args.skip_gene_tables:
print "storing gene-detailed"
loader._get_gene_detailed()
print "storing gene-summary"
loader._get_gene_summary()
if not args.test_mode:
print "updating gene-table"
loader.update_gene_table()
if not args.test_mode:
print "building indices"
loader.build_indices_and_disconnect()
else:
import database
database.close_and_commit(loader.c)
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.store_vcf_header()
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.store_vcf_header()
gemini_loader.populate_from_vcf()
gemini_db.add_max_aaf(gemini_loader.c)
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()
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.store_vcf_header()
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], region_only=False, tempdir=args.tempdir)