parser.add_argument('-y', action="store_true", dest='allyes',
help='assume "yes" to all questions')
parser.add_argument('-f', action="store_true", dest='force',
help='forces download even if the files exist')
parser.add_argument('-s', action="store_true", dest='simulate',
help='simulate and print commands. Nothing is downloaded')
args = parser.parse_args()
if 'all' in args.dbs:
args.dbs = EGGNOG_DATABASES
if args.force or not pexists(pjoin(DATA_PATH, 'eggnog.db')):
if args.allyes or ask("Download main annotation database?") == 'y':
print colorify('Downloading "eggnog.db" at %s...' %DATA_PATH, 'green')
download_annotations()
else:
print 'Skipping'
else:
print colorify('Skipping eggnog.db database (already present). Use -f to force download', 'lblue')
if args.force or not pexists(pjoin(DATA_PATH, 'OG_fasta')):
if args.allyes or ask("Download OG fasta files for annotation refinement (~20GB after decompression)?") == 'y':
print colorify('Downloading fasta files " at %s/OG_fasta...' %DATA_PATH, 'green')
download_groups()
else:
print 'Skipping'
sys.exit(1)
##
if "EGGNOG_DATA_DIR" in os.environ:
set_data_path(os.environ["EGGNOG_DATA_DIR"])
if args.data_dir:
set_data_path(args.data_dir)
data_path = get_data_path()
# http://eggnog5.embl.de/download/eggnog_5.0/e5.proteomes.faa
if not pexists(get_eggnog_proteins_file()):
if args.allyes or ask(
f"Download eggnog5 proteins to {data_path}? ~9GB (It is required to create new databases)"
) == 'y':
print(
colorify(
f'Downloading eggnog5 proteins file to {data_path}...',
'green'))
download_proteins(data_path)
else:
print(
colorify(
f'eggnog5 proteins file was not found. Use --data_dir to specify another data path, or allow the download',
'red'))
sys.exit(1)
else:
print(
colorify(
parser.add_argument('-y', action="store_true", dest='allyes',
help='assume "yes" to all questions')
parser.add_argument('-f', action="store_true", dest='force',
help='forces download even if the files exist')
parser.add_argument('-s', action="store_true", dest='simulate',
help='simulate and print commands. Nothing is downloaded')
args = parser.parse_args()
if 'all' in args.dbs:
args.dbs = EGGNOG_DATABASES
if args.force or not pexists(pjoin(DATA_PATH, 'eggnog.db')):
if args.allyes or ask("Download main annotation database?") == 'y':
print colorify('Downloading "eggnog.db" at %s...' %DATA_PATH, 'green')
download_annotations()
else:
print 'Skipping'
else:
print colorify('Skipping eggnog.db database (already present). Use -f to force download', 'lblue')
if args.force or not pexists(pjoin(DATA_PATH, 'OG_fasta')):
if args.allyes or ask("Download OG fasta files for annotation refinement (~20GB after decompression)?") == 'y':
print colorify('Downloading fasta files " at %s/OG_fasta...' %DATA_PATH, 'green')
download_groups()
else:
print 'Skipping'
if "EGGNOG_DATA_DIR" in os.environ:
set_data_path(os.environ["EGGNOG_DATA_DIR"])
if args.data_dir:
set_data_path(args.data_dir)
# if args.force or not pexists(pjoin(get_data_path(), 'og2level.tsv.gz')):
# print colorify('Downloading "og2level.tsv.gz" at %s' %get_data_path(), 'green')
# download_og2level()
# if 'all' in args.dbs:
# args.dbs = EGGNOG_DATABASES
if args.force or not pexists(pjoin(get_data_path(), 'eggnog.db')):
if args.allyes or ask("Download main annotation database?") == 'y':
print colorify(
'Downloading "eggnog.db" at %s...' % get_data_path(), 'green')
download_annotations()
else:
print 'Skipping'
else:
if not args.quiet:
print colorify(
'Skipping eggnog.db database (already present). Use -f to force download',
'lblue')
# if args.force or not pexists(pjoin(get_data_path(), 'OG_fasta')):
# if args.allyes or ask("Download OG fasta files for annotation refinement (~20GB after decompression)?") == 'y':
# print colorify('Downloading fasta files " at %s/OG_fasta...' %get_data_path(), 'green')
args = parser.parse_args()
if "EGGNOG_DATA_DIR" in os.environ:
set_data_path(os.environ["EGGNOG_DATA_DIR"])
if args.data_dir:
set_data_path(args.data_dir)
data_path = get_data_path()
##
# Annotation DB
if args.force or not pexists(get_eggnogdb_file()):
if args.allyes or ask("Download main annotation database?") == 'y':
print(colorify(f'Downloading "eggnog.db" at {data_path}...', 'green'))
download_annotations(data_path)
else:
print('Skipping')
else:
if not args.quiet:
print(colorify('Skipping eggnog.db database (already present). Use -f to force download', 'lblue'))
##
# NCBI taxa
if args.force or not pexists(get_ncbitaxadb_file()):
if args.allyes or ask("Download taxa database?") == 'y':
print(colorify(f'Downloading "eggnog.taxa.db" at {data_path}...', 'green'))
download_taxa(data_path)