BP_TAXONOMY2TREE(1p)

✨ NAME ✨

okay so bestie, gather round 💖 this is bp_taxonomy2tree — the 1p Perl manual page for building a taxonomic tree based on the full lineages of a set of species names. yes. that's the whole vibe. 🌸

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🌈 DESCRIPTION 🌈

So here's the tea: this script takes the species names you hand it, goes and looks them up in the NCBI Taxonomy database, pulls their full lineage, and then drops them into a Newick taxonomic tree that it just… shows you on screen. iconic behaviour honestly 👑

Like so:

bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s Human
bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s "Homo Sapiens"

Two examples, both slay, both -s-heavy. 💅

You can also throw in -d to say where the index files should live, -o to point at your NCBI nodes file, and -a for the NCBI names file. OR — if you don't have the NCBI flatfiles installed at all — you can use -e to hit up the web-based Entrez taxonomy database instead. no flatfiles, no problem 🦋

Heads up bestie: this script needs the bioperl-run pkg installed too. not optional. it's a requirement. 🫶

Okay and now the part that actually matters: handing over the nodes.dmp and names.dmp files from the NCBI Taxonomy dump (peep Bio::DB::Taxonomy::flatfile for more info on that) is only necessary the first time you run it. After that? You're free. ✨

But lowkey, that first run? It creates the local indexes and it may take quite a long time. Like, go make a snack long. 😭 However — and this is the payoff — once those indexes exist, they give you fast access for species → taxon id lookups OR taxon id → species name lookups. both directions, bestie. ate. 🔥

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💜 AUTHOR — Gabriel Valiente, reimplemented by Sendu Bala 💜

Email valiente@lsi.upc.edu · Email bix@sendu.me.uk

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and that's a wrap on the group chat 🌸 this page was brought to you by perl v5.32.1, dated 2021-08-15 — mwah, take care of her, she's a classic 🎀💖