BP_LOCA...DB_QUERY(1)

🌸 NAME 🌸

Hii bestie 💖 this is the BP_LOCA...DB_QUERY(1) manual page from the User Contributed Perl Documentation, and the icon of the hour is bp_local_taxonomydb_query — a script that queries a local TaxonomyDB for species or taxonid. Periodt. ✨

🦋 DESCRIPTION 🦋

Okay so this script is an example implementation of access to a local Taxonomy database implemented with Berkeley DB — and yes, the DB_File module is needed, no cap. 🫶

Usage:

bp_local_taxonomydb_query.PLS: [-v] --nodes nodes.dmp --names names.dmp "Genus1 species1" "Genus2 species2"

Spot the flags, bestie:

• -v — appears in the usage line; the page doesn't explain more, so I'm not inventing anything. 💀
• --nodes nodes.dmp — the usage line shows it taking nodes.dmp.
• --names names.dmp — the usage line shows it taking names.dmp.

Providing the nodes.dmp and names.dmp files from the NCBI Taxonomy dump (see Bio::DB::Taxonomy::flatfile for more info) is only necessary on the first time running. 👑 This will create the local indexes and may take quite a long time — like, literally be patient, bestie 😭. However once created, these indexes will allow fast access for species to taxon id OR taxon id to species name lookups. That's the whole vibe check. 🦋

Lowkey important: the first run is the slow one because it creates the local indexes; after that, the fast lookups are the main character energy. ✨

Cute sign-off time 🌈: this page comes from perl v5.42.3, dated 2021-02-03, and the footer tag is BP_LOCA...DB_QUERY(1). Byeee, bestie 👑💖