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The **validate** module produces valid record fasta file with taxid attributes. This fasta file works with NCBI taxonomy so that it can be used for further analysis like taxonomic assignment using ecotag.
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### Usage
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#### The simplest case:
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```
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mkbdr validate --fasta raw.fasta --output_prefix res
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```
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This will read the FASTA file `raw.fasta` and check taxonomy and format of each records. Ultimately, mkbdr generates 3 FASTA files, valid records, faulty taxonomy records and faulty format records with `res` as prefix such as:
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```
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res_valid.fasta
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res_faulty_format.fasta
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res_faulty_taxonomy.fasta
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```
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#### Basic curation:
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* To perform curation of names without editing NCBI taxonomy files
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```
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mkbdr validate --fasta raw.fasta --output_prefix res --curate curation_table.csv
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```
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`curation_table.csv` is read to perform curation on species name of records in `raw.fasta`.
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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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```
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mkbdr validate --fasta raw.fasta --output_prefix res --ncbi_taxdump path/to/ncbi_taxo
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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 --output_prefix res --ncbi_taxdump path/to/an/other/ncbi_taxo2
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```
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### Inputs
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### Outputs
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### Options |
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\ No newline at end of file |