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The **curegen** module produces the curation CSV file taking advantage of geonames and ete3 dependencies. This curation CSV file can be use to perform automatic curation with the command `mkbdr validate --curate`.
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# Inputs
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* Faulty taxonomy FASTA file (see description [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#faulty-taxonomy-fasta-file))
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* (optional) NCBI taxonomy files (see description [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#ncbi-taxonomies-file))
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# Command-line Arguments
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This table summarizes the command-line arguments which are using by `mkbdr curegen`.
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| complete flag argument | short flag | Default value | Summary |
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| --- | --- | --- | --- |
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| `--fasta` | `-f` | NA | path of the input faulty taxonomy barcodes sequences FASTA file |
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| `--output_prefix` | `-o` | NA | prefix of the output curation CSV file such as prefix.csv |
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| `--database_globalnames` | `-d` | 'Fishbase Cache' | Name of the selected database from GlobalNames i.e. 'Catalogue of Life' or 'Fishbase Cache' |
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| `--ncbi_taxdump` | `-n` | NA | path of NCBI taxonomy folder |
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| `--ncbi_taxdump_load` | `-l` | FALSE | load NCBI taxonomy from NCBI taxonomy folder path |
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