Commit 2019358a authored by peguerin's avatar peguerin
Browse files

update args list

parent f79c4e0e
......@@ -33,17 +33,18 @@ def parse_args(usage=HELPER_TEXT):
validate = subprasers.add_parser('validate', help='check format and taxonomy')
validate.add_argument("-f","--fasta", type=str, help='path of the barcodes sequences FASTA file', required=True)
validate.add_argument("-c","--curate", type=str, help='path of the curated taxonomy CSV file', required=False, default="NA")
validate.add_argument("-c","--curate", type=str, help='path of the taxonomy curation CSV file. Header must be current_name;ncbi_name;genus;family. A curation CSV file can be generated with the command curegen', required=False, default="NA")
validate.add_argument("-n","--ncbi_taxdump", type=str, help='path of NCBI taxdump.tar.gz file', required=False, default="NA")
validate.add_argument("-o","--output_prefix", type=str, help='prefix of the output FASTA such as [PREFIX].fasta')
curate = subprasers.add_parser('curate', help='try to correct wrong taxonomy')
curate.add_argument("-f","--fasta", type=str, help='path of the barcodes sequences FASTA file', required=True)
curate.add_argument("-o","--output_prefix", type=str, help='prefix of the output curated taxonomy CSV such as [PREFIX].csv')
curegen = subprasers.add_parser('curegen', help='try to correct wrong taxonomy')
curegen.add_argument("-f","--fasta", type=str, help='path of the barcodes sequences FASTA file', required=True)
curegen.add_argument("-n","--ncbi_taxdump", type=str, help='path of NCBI taxdump.tar.gz file', required=False, default="NA")
curegen.add_argument("-o","--output_prefix", type=str, help='prefix of the output curated taxonomy CSV such as [PREFIX].csv')
args = parser.parse_args()
if args.command not in ['validate', 'curate']:
if args.command not in ['validate', 'curegen']:
print(usage)
sys.exit(0)
......
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