diff --git a/src/findMitoReference.py b/src/findMitoReference.py index 7d7defa..8fa4ef6 100644 --- a/src/findMitoReference.py +++ b/src/findMitoReference.py @@ -75,17 +75,20 @@ def find_full_mito(group, outfolder, length_threshold, considered, org_type='mit parser.add_argument('--email', nargs='?', default="") parser.add_argument('--outfolder', nargs='?', default="") parser.add_argument('--type', choices=['mitochondrion','chloroplast'], default='mitochondrion', \ - help='specify the type of organelle') + help='Specify the type of organelle') parser.add_argument('--min_length', nargs='?', type=int, default=0, \ - help='minimal appropriate length') + help='Minimal appropriate length') parser.add_argument('-n', nargs='?', type=int, default=1, \ help='Number of genomes to report. Reported in order of identification') + parser.add_argument('--ncbi-api-key', nargs='?', help='Set NCBI API key') args = parser.parse_args() n = args.n if n < 1: print('Number of genomes to report must be at least 1 (default)') exit(1) Entrez.email = args.email + if args.ncbi_api_key: + Entrez.api_key = args.ncbi_api_key if not os.path.isdir(args.outfolder): os.mkdir(args.outfolder) print('Looking for ' + args.type +' for ' + args.species)