PMRNA(1)

💖 PMRNA — the pmrna(1) glow-up 💖

okay bestie, sit down, hydrate, and let me tell you about pmrna — it's a little user command living in section 1 of your manual, and it's about to become your whole personality. no cap. 🦋

✨ NAME ✨

pmrna — the way it literally just filters out all but the primary isoform from each gene of the input. that's it. that's the job. and it ate. 💅

🌸 SYNOPSIS 🌸

pmrna [options] < annot.gff3 > new.gff3

like, you pipe your annotation in and the filtered goodness comes out the other side. main character pipeline energy, fr fr. 🎀

💜 DESCRIPTION 💜

here's the tea — pmrna takes a GFF3 annotation on stdin and writes a new GFF3 on stdout with only the primary isoform kept per gene. and here are all the Options you can pass, no skips, no shortcuts:

• -h, --help — print this help message and exit. classic. the "i just need to know what i'm doing" button. 🙈
• -i, --introns — a flag saying that introns are declared explicitly and do not need to be inferred from exon features. default behaviour is to infer introns, so only reach for this if your file is already spilling the intron truth itself. 🧚
• -l, --locus — report a single representative mRNA for each locus instead of for each gene. it's giving "zoom out a little, bestie". 👑
• -m, --map: FILE — write each gene/mRNA mapping to the specified file. receipts! keep the paper trail! 🍓
• -p, --pseudogenes — disable pseudogene detection and correction. so by default detection and correction are on, and this flag says "no thank you, i'll handle my own pseudogenes". 💀

heads up, gorgeous: pseudogene detection and correction is on by default, so -p is you actively turning it off. don't come for me, that's just what the flag does. 🫶

that's the whole vibe check, bestie. every option, every default, nothing left behind. now go filter something and slay. 🌈

this lil page is from pmrna version 0.15.1, dated January 2016 — vintage but iconic, like a limited-edition drop. mwah. 💖⭐🌸