PXRLS(1)

📦
version 1.3.2 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💅 PXRLS(1) — the taxon relabelling glow-up 💅

User Commands ✨ pxrls ✨ version 1.3.1 ✨ June 2024

🌸 NAME 🌸

pxrls — taxon relabelling from alignments 🦋

✨ SYNOPSIS ✨

pxrls [OPTIONS]... FILES

🎀 DESCRIPTION 🎀

okay bestie, so pxrls does taxon relabelling for alignments. it's giving glow-up-for-your-taxa 💖

it'll take fasta, phylip, and nexus formats — from a file or from STDIN, your choice, we're flexible like that. 🌈

now here's the tea: you gotta give it two ordered lists of taxa, fr fr:

  • -c — the current labels
  • -n — the new labels

OR (not me giving you options 💅) you can hand it a regex pattern -p plus some replacement text -r instead. either way, it works.

and the results? written out in fasta format. periodt. 👑

💅 OPTIONS 💅

  • -s, --seqf=FILE — the input seq file, bestie. if you don't give one, it reads from STDIN instead. no pressure. 🫶
  • -c, --cnames=FILE — the file holding your current taxon labels, one per line. this is the before pic. 📸
  • -n, --nnames=FILE — the file holding your new taxon labels, one per line. and this is the after. ✨
  • -p, --pattern=STRING — a regex pattern to replace. regex girlies rise. 🔥
  • -r, --replace=STRING — the replacement pattern. the glow-up text itself. 💖
  • -v, --verbose — makes the output more verbose. it will simply talk more. and honestly? relatable. 😭
  • -o, --outf=FILE — the output file. if you don't give one, it goes to STOUT instead. (yes. STOUT. we said what we said. 💀)
  • -h, --help — displays this help and exits. your little helper 🧚
  • -V, --version — displays the version and exits. main character energy, honestly ⭐
  • -C, --citation — displays the phyx citation and exits. cite your sources, babes, it's the bare minimum 🎀

📚 CITATION 📚

Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.

like. iconic. cite it. 🫶

👑 AUTHOR 👑

Written by Joseph W. Brown, Stephen A. Smith (blackrim)

🐛 REPORTING BUGS 🐛

found a bug? first of all, not the vibe. 😭 report it to:

https://github.com/FePhyFoFum/phyx/issues

phyx home page: https://github.com/FePhyFoFum/phyx

Copyright © 2016-2024 FePhyFoFum — License GPLv3

and that's the whole page, bestie 🦋💖✨

this was pxrls 1.3.1, dated June 2024 — go relabel some taxa, you absolute icon 👑🌸💅

📦 where this page comes from