GENEPARSE(1)

💖 GENEPARSE — ok bestie, listen up 💖

geneparse, and yes it's a sequence file loader frontend — say that five times fast. It's literally the lil doorway that loads your sequence files and sends them somewhere cute. 🧬✨

✨ SYNAPSE ✨

geneparse [options...] [input] [input2 ...] #read input and write to stdout

Reads your input, writes it to stdout, that's the whole vibe. 💅

🌸 DESCRIPTION 🌸

So basically: it reads a sequence file and writes it somewhere. Default somewhere = stdout. Simple. Iconic. 🫶

You can also grab a specific range inside an input file by writing file[start,stop]. And get this — the square brackets can be swapped for any of {[()]}, so genome.fa[3000,4000] and genome.fa{3000~4000} are both valid and both slay. 😭

🚨 okay but real talk — all of those might be parsed by your shell. So quote that thing or your shell is gonna eat it before geneparse ever sees it. Not cute.

Also! Any non-word character can be used to separate the numbers. Live your truth. 🌈

🎀 OPTIONS 🎀

• --repeatmask, -r — use soft-repeatmasked sequences, aka swap the lowercase bases out for N's. lowercase who? never met her. 💀
• --upper, --unmask, -U — uppercase ALL the bases. every single one. 📣
• --length, -l — just print the length and dip. that's it, that's the whole job. ✨
• --clean, -c — don't append a new line when it's finished. no trailing lil guy. 🙈
• --version, -V — prints the program version. 👑
• --help, -h — prints a help message. your bestie when you're lost fr fr. 🫶
• --output, -o — send output to a file (otherwise it goes to stdout). heads up: --output implies --clean. 🤝
• --quiet, -q — silence all warnings. shhh. nothing to see here. 🤫
• --verbose, -v — prints lots of extra details. main character energy, it will NOT be brief. 🗣️

📜 LICENSE 📜

GNU General Public License, version 3 (GPLv3). 🩷

🌐 AVAILABILITY 🌐

http://murasaki.sourceforge.net

👑 AUTHOR 👑

Kris Popendorf <krisp@dna.bio.keio.ac.jp> — thank you for your service king 🫡✨

🦋 SEE ALSO 🦋

• murasaki(1)
• geneparse(1)

(yes, geneparse is in its own SEE ALSO. self-love. we stan. 💅)

and that's the whole page bestie!! this one's living in the perl v5.10.1 era, dated 2010-05-31 — a vintage icon, no cap. mwah 💋🌸