EXONPAIRS(1)

💖 EXONPAIRS 💖

okay bestie, so exonpairs is literally a SNAP module and it's here to do gene-finding stuff with HMMs and FASTA files, and honestly? it ate. ✨

🦋 NAME 🦋

exonpairs — the SNAP module named exonpairs. that's it, that's the name, no cap. 💅

🌸 SYNOPSIS 🌸

exonpairs [options] <HMM file> <FASTA file> [options]

notice how [options] shows up twice?? yeah. before and after the files. iconic behaviour, we don't question it, we just respect it. 👑

✨ OPTIONS ✨

one bullet per flag, bestie, and the numbers in [] are the defaults — don't come for me, come for the docs.

• -min-intron <int> — shortest intron length you'll tolerate. default [30]. like, anything tinier is giving "not an intron" 💀
• -max-intron <int> — longest intron length allowed. default [10000]. big intron energy, but not that big.
• -einit-length <int> — minimum Einit length, measured in bp. default [10].
• -eterm-length <int> — minimum Eterm length, measured in bp. default [10].
• -exon-length <int> — minimum Exon length, measured in bp. default [30].
• -intron-score <float> — minimum Intron score, in bits. default [-5].
• -einit-score <float> — minimum Einit score, in bits. default [-5].
• -eterm-score <float> — minimum Eterm score, in bits. default [-5].
• -exon-score <float> — minimum Exon score, in bits. default [-5].
• -pair-score <float> — minimum pair score, and the pair is exon-intron-exon, so it's the whole trio being judged together. default [10].
• -flank-length <int> — how much flanking sequence you get per exon. default [20].
• -lcmask — treat lowercase as N. that's the whole vibe. lowercase letters stop being letters and start being N. 🙈

🌈 quick reminder bestie: every one of those defaults is exactly what's written, so if you change a number, that's on you. don't blame the module. 🫶

💜 SEE ALSO 💜

ngl there's no SEE ALSO section in this one, so instead here's a vibe check: go read the other SNAP module pages, they're all in the same family. 💖

exonpairs 2010-07-28 — that's the source/version, born way back, still slaying. and the date on the page? October 2013. so yeah, this manual is vintage, and vintage is timeless. 🎀🦋⭐💅🧚🍓