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* To run mkbdr with your own NCBI taxonomy located at path/to/ncbi_taxo you have to add the argument `--ncbi_taxdump_load` to your command for the first time:
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```
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mkbdr validate --fasta raw.fasta --output_prefix res --ncbi_taxdump path/to/ncbi_taxo --ncbi_taxdump_load
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mkbdr validate --fasta raw.fasta \
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--output_prefix res \
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--ncbi_taxdump path/to/ncbi_taxo \
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--ncbi_taxdump_load
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```
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ete3 will load the files located in `path/to/ncbi_taxo` and stores the NCBI taxonomy tree object in your home folder. Once the NCBI taxonomy is locally loaded, you can simply run the command:
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```
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mkbdr validate --fasta raw.fasta --output_prefix res --ncbi_taxdump path/to/an/other/ncbi_taxo2 --ncbi_taxdump_load
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mkbdr validate --fasta raw.fasta \
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--output_prefix res \
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--ncbi_taxdump path/to/an/other/ncbi_taxo2 \
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--ncbi_taxdump_load
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```
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#### Using a local NCBI taxonomy, performs a curation which add new species to your local taxonomy
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* To run mkbdr in order to add new species, you have to allow edition of local NCBI taxonomy files with the argument `--ncbi_taxdump_edition`. To specify the location of NCBI taxonomy folder to edit, add the argument `--ncbi_taxdump`. To apply a curation, add the argument `--curate`. Thorough description of curation CSV file is available [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#curation-file).
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The following curation CSV gives instruction to MKBDR to create a new custom species called _Distichodus perspicillatus_ with genus _Distichodus_ family _Distichodontidae_.
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`curation_new_species.csv`:
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```
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current_name;ncbi_name;genus;family;ncbi_rank;method
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Distichodus perspicillatus;NA;Distichodus;Distichodontidae;genus;Catalogue of Life
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... | ... | @@ -93,7 +101,12 @@ Distichodus perspicillatus;NA;Distichodus;Distichodontidae;genus;Catalogue of Li |
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The MKBDR complete command is:
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```
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mkbdr validate --fasta raw.fasta --output_prefix res --ncbi_taxdump path/to/ncbi_taxo --ncbi_taxdump_load --ncbi_taxdump_edition
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mkbdr validate --fasta raw.fasta \
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--output_prefix res \
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--curate curation_new_species.csv \
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--ncbi_taxdump path/to/ncbi_taxo \
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--ncbi_taxdump_load \
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--ncbi_taxdump_edition
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```
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This will edit NCBI taxonomy files located on `path/to/ncbi_taxo` adding a new custom species _Distichodus perspicillatus_. This species records will be generated with custom taxid in valid FASTA file output called `res_valid.fasta`.
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