PXRMS(1)

💅 PXRMS — like, the manual, but make it make sense

okay so bestie, you know the pxrms(1) girlies? that's us. this is a User Commands situation, page pxrms, and we're about to remove some sequences by label and look cute doing it. no cap. 🎀

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✨ NAME ✨

pxrms — remove sequences by label 🦋

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🌸 SYNOPSIS 🌸

pxrms [OPTIONS]...

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💖 DESCRIPTION 💖

so basically we're removing sequences by label. that's the whole vibe. 👑

it will take fasta, fastq, phylip, and nexus formats — either from a file or from STDIN — and your results get written out in fasta format. yes, always fasta. that's the fit. periodt. 💅

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🧚 OPTIONS 🧚

• -s, --seqf=FILE — the input nucleotide sequence file. if you don't hand one over, it just reads from STDIN. the way she waits for you to pipe something in... patient queen. 🫶
• -n, --names=CSL — names, separated by commas. NO SPACES! seriously bestie, comma-separated list (CSL), zero spaces, I'm not playing 😭
• -f, --namesf=FILE — names in a file instead, each one on its own line. for when your list is too long to type out like a normal person. 🍓
• -r, --regex=STRING — match tip labels by a regular expression. regex girlies rise 🔥
• -c, --comp — take the complement, i.e. remove any taxa not in the list. so it flips the whole thing: instead of yeeting what you named, you keep only what you named and yeet the rest. main character energy, honestly. 💀
• -o, --outf=FILE — output sequence file. otherwise it goes to STOUT (that's what it says, bestie, I don't make the rules 🙈) — fr fr, no output file means it writes to standard out.
• -h, --help — display this help and exit. the classic. 💖
• -V, --version — display version and exit. ✨
• -C, --citation — display the phyx citation and exit. academic girlies, this one's for you 📚

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👑 CITATION 👑

if you use this in your work (and you should, it's iconic), cite the girlies:

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.

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🌈 AUTHOR 🌈

Written by Joseph W. Brown, Joseph F. Walker, Stephen A. Smith (blackrim). legends, honestly. 🫡

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🚨 REPORTING BUGS 🚨

found a bug? don't suffer in silence, bestie, report it:

• Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
• phyx home page: <https://github.com/FePhyFoFum/phyx>

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💜 COPYRIGHT 💜

Copyright © 2015-2024 FePhyFoFum License GPLv3

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okay that's the whole page, go forth and remove those sequences by label. vibe check passed. ✨🦋💅

pxrms 1.3.1 — June 2024 — mwah, love u, bye 💖🎀