def get_eggnog_taxid_info_file():
return pjoin(get_data_path(), "e5.taxid_info.tsv")
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'
def get_eggnog_proteins_file():
return pjoin(get_data_path(), "e5.proteomes.faa")
download_taxid_info(data_path)
else:
print(
colorify(
f'eggnog5 taxid info table was not found. Use --data_dir to specify another data path, or allow the download',
'red'))
sys.exit(1)
else:
print(
colorify(
f'Using existing eggnog5 taxid info table found at {get_eggnog_taxid_info_file()}',
'green'))
taxa_set = parse_taxa_table(get_eggnog_taxid_info_file(), args.taxids,
args.taxa)
proteins_out_file = pjoin(get_data_path(), f"{args.dbname}.faa")
parse_proteins(proteins_out_file, get_eggnog_proteins_file(), taxa_set)
# generate DB
dbprefix = None
if args.mode == "diamond":
dbprefix = pjoin(get_data_path(), f'{args.dbname}.dmnd')
create_diamond_db(dbprefix, proteins_out_file)
elif args.mode == "mmseqs":
dbdir = pjoin(get_data_path(), f'{args.dbname}.mmseqs')
dbprefix = pjoin(get_data_path(), f'{args.dbname}.mmseqs',
f'{args.dbname}.mmseqs')
if not os.path.isdir(os.path.realpath(dbdir)):
os.mkdir(dbdir)
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)
# 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':
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'
parser.add_argument('-q',
action="store_true",
dest='quiet',
help='quiet_mode')
parser.add_argument("--data_dir",
metavar='',
type=existing_dir,
help='Directory to use for DATA_PATH.')
args = parser.parse_args()
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'