... | @@ -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
|
|
```
|
|
```
|
|
|
|
|
... | | ... | |