Commit 7f53813b authored by peguerin's avatar peguerin
Browse files

args database_globalnames

parent c172c66b
...@@ -59,7 +59,7 @@ def main(): ...@@ -59,7 +59,7 @@ def main():
print(report_validate_results(results)) print(report_validate_results(results))
elif args.command == 'curegen': elif args.command == 'curegen':
print('curation generation...') print('curation generation...')
curegenDf = generate_curation_df(args.fasta, ncbi) curegenDf = generate_curation_df(args.fasta, ncbi, args.database_globalnames)
print(curegenDf) print(curegenDf)
curegenDf.to_csv(str(args.output_prefix)+'_curation.csv', index = None, sep = ';') curegenDf.to_csv(str(args.output_prefix)+'_curation.csv', index = None, sep = ';')
else: else:
......
...@@ -40,6 +40,7 @@ def parse_args(usage=HELPER_TEXT): ...@@ -40,6 +40,7 @@ def parse_args(usage=HELPER_TEXT):
curegen = subprasers.add_parser('curegen', help='try to correct wrong taxonomy') 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("-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("-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') curegen.add_argument("-o","--output_prefix", type=str, help='prefix of the output curated taxonomy CSV such as [PREFIX].csv')
args = parser.parse_args() args = parser.parse_args()
......
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