Taxonomy.jl
Taxonomy.jl is a julia package to handle NCBI-formatted taxonomic databases. The main features are:
- Convert a name to taxids
- Traverse taxonomic subtrees from a given taxon
- Compute the lowest common ancestor (LCA) of given taxons
- Evaluate ancestor/descendant relationships between two taxa
- Filter taxa by rank range
- Construct taxonomic lineage of the given taxon
- Reformat lineage according to canonical ranks
- Construct a
DataFrame
from lineages
Now, this package only supports scientific name
.
Installation
Install Taxonomy.jl as follows:
julia -e 'using Pkg; Pkg.add("Taxonomy")'
Download database
You need to download taxonomic data from NCBI's servers.
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
tar xzvf taxdump.tar.gz