update args list

mkbdr/arguments.py

@@ -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)