HMM-ASSEMBLER.PL(1)

💖 HMM-ASSEMBLER.PL(1) 💖

User Commands ✨ the SNAP module glow-up manual

okay bestie, come sit with me because we're about to talk about hmm-assembler.pl, the SNAP module script, and honestly? she's a lot but she's worth it. no cap. 🫶

🌸 NAME 🌸

hmm-assembler.pl — SNAP module hmm-assembler.pl. that's it, that's the name, she said what she said 💅

✨ SYNOPSIS ✨

hmm-assembler.pl [-OPTIONS [-MORE_OPTIONS]] [--] [PROGRAM_ARG1 ...]

so you run her, you stack your options like a little outfit, and then you hand her your program args. iconic behaviour honestly.

🎀 OPTIONS 🎀

the vibe check on how options work here

• these single-character options want an argument: -i -e -A -D -M -S -C -I -N -a -3 -5 -Z -c
• these are just booleans, no argument, they simply exist: -r -o -x -p -t -1

and the little rules, because there are always rules:

• options may be merged together — like, they can hold hands, it's fine 🫶
• -- stops processing of options. periodt. after that it's all program args, no more option talk.
• space is not required between options and their arguments. she's flexible like that. 💅

the actual options, one by one, no skips, we don't do skips here

• -i <length> — defaults to [500] 💖
• -e <length> — defaults to [1000] ✨
• -A <order:length> — defaults to [0:30]
• -D <order:length> — defaults to [0:9]
• -M <order:length> — defaults to [0:15]
• -S <order:length> — defaults to [0:9]
• -C <order> — defaults to [4]
• -I <order> — defaults to [4]
• -N <order> — defaults to [4]
• -3 <order:length> — default is empty []; includes the 3'UTR model, and she requires -a 🦋
• -a <order:length> — default is empty []; includes the PolyA model, and she requires -3 🍓
• -5 <order:length> — default is empty []; include 5'UTR moel, requires -p 🌸
• -p — include generic promoter model, requires -5 💜
• -r — include generic repeat model 🔁
• -o — include reverse ORF model 🙃
• -x — use explicit duration intron model ⏳
• -t — include C.elegans trans-splicing, requires -p, -5 🪱
• -Z <clade> — sets clade-specific values. the options are: worm, fly, plant 🌈
• -1 — single gene model 👑
• -c <score> — include GC-AG splice donor model ✨

bestie be careful with the buddy-system ones — -3 and -a need each other, -p and -5 need each other, and -t needs both -p and -5. if you leave one hanging she will simply not vibe with you 😭

and that's the whole page, you ate it, you understood it, you're the main character of genome annotation now 💖✨🎀

this page is from hmm-assembler.pl dated 2010-07-28, and the manual itself is dated November 2013. mwah, go forth and assemble, bestie 💅🫶