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 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:
from gemini 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:
from gemini import database
database.close_and_commit(loader.c)