[](https://circleci.com/gh/pvanheus/ncbitaxonomy)
### ncbitaxonomy
This is a Rust crate (i.e. library) for working with a local copy of the
[NCBI Taxonomy database](https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/).
The database can be downloaded (either `taxdump.zip` or `taxdump.tar.gz`) from the
[NCBI Taxonomy FTP site](https://ftp.ncbi.nih.gov/pub/taxonomy/).
Documentation for version 0.1.3 is available at [crates.io](https://docs.rs/ncbitaxonomy/0.1.3/ncbitaxonomy/struct.NcbiTaxonomy.html).
### taxonomy_filter_refseq
(new in 0.1.1)
A tool to filter a NCBI RefSeq FASTA file so that only the ancestors of a given taxon
are retained.
```bash
$ taxonomy_filter_refseq --help
taxonomy_filter_refseq 0.1.2
Peter van Heusden <pvh@sanbi.axc.za>
Filter NCBI RefSeq FASTA files by taxonomic lineage
USAGE:
taxonomy_filter_refseq [OPTIONS] <INPUT_FASTA> <TAXONOMY_DIR> <ANCESTOR_NAME> [OUTPUT_FASTA]
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-t, --tax_prefix <TAXONOMY_FILENAME_PREFIX> String to prepend to names of nodes.dmp and names.dmp
ARGS:
<INPUT_FASTA> FASTA file with RefSeq sequences
<TAXONOMY_DIR> Directory containing the NCBI taxonomy nodes.dmp and names.dmp files
<ANCESTOR_NAME> Name of ancestor to use as ancestor filter
<OUTPUT_FASTA> Output FASTA filename (or stdout if omitted)
```
### TODO
* Refactor taxonomy_filter_refseq: move most code to library, add tests