... | ... | @@ -56,7 +56,7 @@ mkbdr validate --fasta raw.fasta --output_prefix res --curate curation_table.csv |
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### Using a local NCBI taxonomy:
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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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* 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:
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```
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mkbdr validate --fasta raw.fasta \
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... | ... | @@ -65,25 +65,7 @@ mkbdr validate --fasta raw.fasta \ |
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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
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```
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The default ncbi taxonomy handled by mkbdr is now your local NCBI taxonomy.
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If you want to change your local NCBI taxonomy again. For instance you want to load the taxonomies located at `path/to/an/other/ncbi_taxo2`:
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```
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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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ete3 will load the files located in `path/to/ncbi_taxo` and stores the NCBI taxonomy tree object in your home folder.
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### Using a local NCBI taxonomy, performs a curation which add new species to your local taxonomy:
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