ncbitaxonomy 0.1.1

Read NCBI Taxonomy Database from files and work with NCBI Taxonomy DB

ncbitaxonomy

This is a Rust crate (i.e. library) for working with a local copy of the NCBI Taxonomy database. The database can be downloaded (either taxdump.zip or taxdump.tar.gz) from the NCBI Taxonomy FTP site.

Documentation for version 0.1.0 is available at crates.io.

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.

$ taxonomy_filter_refseq
error: The following required arguments were not provided:
    <INPUT_FASTA>
    <TAXONOMY_DIR>
    <ANCESTOR_NAME>

USAGE:
    taxonomy_filter_refseq [OPTIONS] <INPUT_FASTA> <TAXONOMY_DIR> <ANCESTOR_NAME> [OUTPUT_FASTA]

TODO

  • Clean up non-idiomatic code (e.g. the use of the insert_new_entry bool)
  • Add testing via CI
  • Refactor taxonomy_filter_refseq: move most code to library, add tests