PYFASTX(1)

💖 PYFASTX 💖

okay bestie, pull up a chair, we're doing the pyfastx manual page (it lives in section 1 of the manual, the User Commands zone, and it's literally about to become your whole personality) 🎀

✨ NAME ✨

pyfastx — fast random access to sequences from FASTA/Q file 🦋

🌸 DESCRIPTION 🌸

usage, babes:

pyfastx COMMAND [OPTIONS]

it's a command line tool for FASTA/Q file manipulation, and yes it's giving main character energy fr fr 💅

🫶 options:

• -h, --help — show this help message and exit. the classic. the icon. use it when you're lost (you won't be, i got you)
• -v, --version — show program's version number and exit. little peek at what you're running, slay

👑 Commands:

• index — build index for fasta/q file. do this first, trust, it's the whole point of "fast random access" 🏃♀️💨
• stat — show detailed statistics information of fasta/q file. numbers. gorgeous numbers 📊
• split — split fasta/q file into multiple files. one file in, many files out, it's giving mitosis 🧬
• fq2fa — convert fastq file to fasta file. glow-up but for file formats ✨
• subseq — get subsequences from fasta file by region. just the lil piece you wanted 🍓
• sample — randomly sample sequences from fasta or fastq file. chaos, but make it reproducible 🎲
• extract — extract full sequences or reads from fasta/q file. the full thing, no crumbs 💜

🌈 SEE ALSO 🌈

every single subcommand has its own on line help, and you can go ask for it, for instance with:

$ pyfastx index --help
usage: pyfastx index [-h] [-f] fastx [fastx ...]

positional arguments:
  fastx       fasta or fastq file, gzip support

options:
  -h, --help  show this help message and exit
  -f, --full  build full index, base composition will be calculated

not me showing you a whole example just to flex that -f, --full builds a full index and calculates base composition 😭 note that one down bestie

and if you want the actually complete documentation (like, the whole novel, not the trailer), look up /usr/share/doc/pyfast/README.rst 📖

and that's the page!! this was pyfastx version 0.8.4, from November 2022, and it's the PYFASTX(1) manual page — go build an index and live your best life, ily 💖✨🎀🦋