... | ... | @@ -8,17 +8,23 @@ The **init_ncbi_taxdump** module download and decompress the NCBI taxdump archiv |
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| complete flag argument | short flag | Default value | Summary |
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| --- | --- | --- | --- |
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| `--folder_path` | `-f` | current working directory | Folder path where to download and decompress the NCBI taxdump archive |
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| `--folder_path` | `-f` | current working directory | Folder path where to download the NCBI taxdump archive |
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| `--decompress` | `-d` | FALSE | Decompress the archive |
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# Example of commands
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This command will download the latest NCBI taxonomy files at the address ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/ and decompress these files into the folder `path/to/local/ncbi_taxo`
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This command will download the latest NCBI taxonomy files at the address ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/ into the target folder `path/to/local/ncbi_taxo`
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```
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mkbdr init_ncbi_taxdump --folder_path path/to/local/ncbi_taxo
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```
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Download and decompress NCBI taxdump archive into the folder `path/to/local/ncbi_taxo`
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```
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mkbdr init_ncbi_taxdump --folder_path path/to/local/ncbi_taxo --decompress
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```
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# Outputs
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Local NCBI Taxonomy files can be useful if you need to add new custom species to the tree of life and need to edit a local taxonomy.
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