def load(parser, args):
if (args.db is None or args.vcf is None):
parser.print_help()
exit("ERROR: load needs both a VCF file and a database file\n")
annos = annotations.get_anno_files(args)
# force skipping CADD and GERP if the data files have not been installed
if args.skip_cadd is False:
if 'cadd_score' not in annos:
sys.stderr.write("\nCADD scores are not being loaded because the"
" annotation file could not be found.\n"
"`Run gemini update --dataonly --extra cadd_score`"
" to install the annotation file.\n\n")
args.skip_cadd = True
else:
sys.stderr.write("CADD scores are being loaded (to skip use:--skip-cadd).\n")
if args.skip_gerp_bp is False:
if 'gerp_bp' not in annos:
sys.stderr.write("\nGERP per bp is not being loaded because the annotation file"
" could not be found.\n Run `gemini update --dataonly --extra gerp_bp`"
" to install the annotation file.\n\n")
args.skip_gerp_bp = True
else:
sys.stderr.write("GERP per bp is being loaded (to skip use:--skip-gerp-bp).\n")
# collect of the the add'l annotation files
annotations.load_annos(args)
l = None
if args.scheduler:
load_ipython(args)
elif args.cores > 1:
load_multicore(args)
else:
l = load_singlecore(args)
finish(args, l)
def load(parser, args):
if (args.db is None or args.vcf is None):
parser.print_help()
exit("ERROR: load needs both a VCF file and a database file\n")
annos = annotations.get_anno_files(args)
# force skipping CADD and GERP if the data files have not been installed
if args.skip_cadd is False:
if 'cadd_score' not in annos:
sys.stderr.write("\nCADD scores are not being loaded because the"
" annotation file could not be found.\n"
"`Run gemini update --dataonly --extra cadd_score`"
" to install the annotation file.\n\n")
args.skip_cadd = True
else:
sys.stderr.write("CADD scores are being loaded (to skip use:--skip-cadd).\n")
if args.skip_gerp_bp is False:
if 'gerp_bp' not in annos:
sys.stderr.write("\nGERP per bp is not being loaded because the annotation file"
" could not be found.\n Run `gemini update --dataonly --extra gerp_bp`"
" to install the annotation file.\n\n")
args.skip_gerp_bp = True
else:
sys.stderr.write("GERP per bp is being loaded (to skip use:--skip-gerp-bp).\n")
# collect of the the add'l annotation files
annotations.load_annos(args)
l = None
if args.scheduler:
load_ipython(args)
elif args.cores > 1:
load_multicore(args)
else:
l = load_singlecore(args)
finish(args, l)
def get_gemini_files(data):
"""Enumerate available gemini data files in a standard installation.
"""
try:
from gemini import annotations, config
except ImportError:
return {}
return {"base": config.read_gemini_config()["annotation_dir"], "files": annotations.get_anno_files().values()}
def get_gemini_files(data):
"""Enumerate available gemini data files in a standard installation.
"""
try:
from gemini import annotations, config
except ImportError:
return {}
return {"base": config.read_gemini_config()["annotation_dir"],
"files": annotations.get_anno_files().values()}