args database_globalnames

mkbdr/__main__.py

@@ -59,7 +59,7 @@ def main():
         print(report_validate_results(results))
     elif args.command == 'curegen':
         print('curation generation...')
-        curegenDf = generate_curation_df(args.fasta, ncbi)
+        curegenDf = generate_curation_df(args.fasta, ncbi, args.database_globalnames)
         print(curegenDf)
         curegenDf.to_csv(str(args.output_prefix)+'_curation.csv', index = None, sep = ';')
     else:

mkbdr/arguments.py

@@ -40,6 +40,7 @@ def parse_args(usage=HELPER_TEXT):
     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("-d","--database_globalnames", type=str, help="Name of the selected database from GlobalNames i.e. 'Catalogue of Life' or 'Fishbase Cache'", required=False, default='FishBase Cache')
     curegen.add_argument("-o","--output_prefix", type=str, help='prefix of the output curated taxonomy CSV such as [PREFIX].csv')
 
     args = parser.parse_args()