ELPH(1)

📦
version 1.0.1 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 NAME 💖

elph — bestie, it's ELPH. That's it, that's the name. 👑

✨ DESCRIPTION ✨

Okay so picture this: ELPH stands for Estimated Locations of Pattern Hits, and it's a motif finder program. That's the whole vibe. It goes looking for patterns and it finds them. Slay. 🦋

Here's how you actually call it, no cap:

elph <multi-fasta_file> [options]

OR, if you're feeling extra and want two files in the mix:

elph <multi-fasta_file-1> <multi-fasta_file-2> [-t <matrix>]

🎀 OPTIONS 🎀

Like, all of them. Every single one. We're not skipping a thing, bestie.

  • -h — prints this help. Your little "what do I even do" button. 🙈
  • -b — just the brief results; it will not print the motif. Minimalist era. 💅
  • -d — finds significance deterministically. No randomness, just vibes with receipts.
  • -v — finds the motif deterministically too. Same energy, different mission.
  • -o <out_file> — writes the output into <out_file> instead of stdout. Redirecting, but make it fashion. ✨
  • -m <motif> — use the given pattern <motif> to compute its best fit matrix to the data. Give it a pattern, it'll find the glow-up. 🔥
  • -a — use aac residues; default is nucleotides residues. Swap the alphabet, keep the drama.
  • -s <seed> — sets the seed for the random generation. Determinism girlies, this one's for you. 🌱
  • -p n — n = no of iterations before deciding local maximum; plateau period variable. Basically "how long do I keep staring before I decide this is the peak".
  • -x — print maximum positions within sequences. Location reveal. 📍
  • -g — find significance of the motif. Is it real or is it just noise? Vibe check. 👀
  • -t <matrix> — test if there is significant difference between the two input files for a given motif matrix; <matrix> is the file containing the motif matrix. Two files enter, one significance test leaves. ⚔️
  • -l — compute Least Likely Consensus (LLC) for the given motif. The anti-consensus. The villain arc. 💀
  • -r — in conjunction with the -m option: the motif is not necessarily in the closest edit distance from the input motif. It's allowed to wander. 🧚
  • -e — only when an additional file is used to test the significance of the motif: find only the motifs that exactly match the input pattern (the -m or -t options). Exact match or nothing, periodt.
  • -n [0..5] — degree of Markov chain used to generate the random file used to test the significance of the motif. default = 2. Range is 0..5, stay in your lane.
  • LEN=n — n = length of motif. How long is the pattern, bestie?
  • ITERNO=n — n = no of iterations to compute the global maximum; default = 10.
  • MAXLOOP=n — n = no of iterations to compute the local maximum; default = 500.
  • SGFNO=n — n = no of iterations to compute significance of motif; default = 1000.
Heads up fr fr: those last four — LEN, ITERNO, MAXLOOP, SGFNO — are written as NAME=n, not as dash-flags. Don't come at me, that's just how it is. 💖

🌈 SEE ALSO 🌈

The full documentation for elph is maintained as a Texinfo manual. If the info and elph programs are properly installed at your site, this command:

info elph

should give you access to the complete manual. Go read it, it's giving ✨educated✨.

And that's the whole page, bestie!! 🫶 This was elph version 1.0.1, from June 2020 — a whole era, honestly. Go find some motifs. You're the main character. 👑🌸

📦 where this page comes from