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)