PXVCF2FA(1)

🌸 PXVCF2FA(1) 🌸

okay bestie, gather round, because this is pxvcf2fa, a little User Command from the phyx family, and she is here to do exactly one iconic thing: turn your vcf into fasta. 💅

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✨ NAME ✨

pxvcf2fa — convert vcf file to fasta 🧬➡️📄

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🦋 SYNOPSIS 🦋

pxvcf2fa [OPTIONS]...

like… that's it. that's the whole vibe. options go in, fasta comes out. ✨

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💖 DESCRIPTION 💖

So basically: convert vcf file to fasta. no cap, that's the whole job.

ngl there's a tiny little catch though — right now she only handles haploid data. phased data will come soon, she's still cooking, be patient with her. 🙈

and the best part? your data can be read from a file or from STDIN, so pipe it in however you like, bestie. 🫶

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👑 OPTIONS 👑

• -s, --seqf=FILE — your input vcf file goes here. if you don't give her one, she'll read from STDIN instead. 🌈
• -u, --uppercase — export the characters in UPPERCASE. shout it, periodt. 🔥
• -o, --outf=FILE — where the output fasta sequence file should go. otherwise it's STOUT. 💜
• -h, --help — display this help and exit. classic, we love a helpful queen. 🎀
• -V, --version — display version and exit. she'll tell you who she is. ⭐
• -C, --citation — display phyx citation and exit. cite your sources, bestie, it's giving academic integrity. 👑

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📚 CITATION 📚

if you use this, you GOTTA cite it, fr fr:

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. absolute legend behaviour. 💖

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🐛 REPORTING BUGS 🐛

found a bug? don't just sit there crying (valid tho 😭), 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 © 2013-2024 FePhyFoFum License GPLv3

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okay that's the whole page bestie, go convert some vcfs and slay 🦋✨ this was pxvcf2fa 1.3.1 from June 2024, mwah 💋🫶