Update Curegen authored by peguerin's avatar peguerin
...@@ -14,8 +14,7 @@ This table summarizes the command-line arguments which are using by `mkbdr cureg ...@@ -14,8 +14,7 @@ This table summarizes the command-line arguments which are using by `mkbdr cureg
| `--fasta` | `-f` | NA | path of the input faulty taxonomy barcodes sequences FASTA file | | `--fasta` | `-f` | NA | path of the input faulty taxonomy barcodes sequences FASTA file |
| `--output_prefix` | `-o` | NA | prefix of the output curation CSV file such as prefix.csv | | `--output_prefix` | `-o` | NA | prefix of the output curation CSV file such as prefix.csv |
| `--database_globalnames` | `-d` | 'Fishbase Cache' | Name of the selected database from GlobalNames i.e. 'Catalogue of Life' or 'Fishbase Cache' | | `--database_globalnames` | `-d` | 'Fishbase Cache' | Name of the selected database from GlobalNames i.e. 'Catalogue of Life' or 'Fishbase Cache' |
| `--ncbi_taxdump` | `-n` | NA | path of NCBI taxonomy folder | | `--ncbi_taxdump_load` | `-l` | NA | load NCBI taxonomy from NCBI taxonomy folder path |
| `--ncbi_taxdump_load` | `-l` | FALSE | load NCBI taxonomy from NCBI taxonomy folder path |
# Example of commands # Example of commands
...@@ -47,7 +46,6 @@ It is possible to load local NCBI taxonomy files. Here we load `path/to/ncbi_tax ...@@ -47,7 +46,6 @@ It is possible to load local NCBI taxonomy files. Here we load `path/to/ncbi_tax
``` ```
mkbdr curegen --fasta test_raw_faulty_taxon.fasta \ mkbdr curegen --fasta test_raw_faulty_taxon.fasta \
--output_prefix "cure" \ --output_prefix "cure" \
--ncbi_taxdump path/to/ncbi_taxo \
--ncbi_taxdump_load --ncbi_taxdump_load
``` ```
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