PBSENCODE(1)

📦 version 1.8, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 NAME 💖

pbsEncode — bestie, this makes an approximate binary encoding of a probabilistic biological sequence (aka a PBS). That's the whole job. She's focused. She's booked. 💅

✨ DESCRIPTION ✨

Okay so here's the tea: pbsEncode produces an approximate binary encoding of a probabilistic biological sequence (PBS), and that PBS is defined by a text file — we're calling it input.probs 🫶

And what does that file look like? Literally this:

  • one row for each position in the sequence
  • one column for each base

So the (i,j)th value in that table? That's the probability of base j at position i. Simple as. No cap. 🧚

The columns should be white-space delimited — don't get cute with commas, bestie, it's whitespace or nothing.

The encoding itself is as defined by codefile, and that file should be in the format used by pbsTrain. iykyk. 🔥

And the iconique detail: this program performs the inverse function of pbsDecode. They're giving duo. They're giving mirror. They're giving "you complete me" but make it bioinformatics. 😭💖

🌸 EXAMPLE 🌸

Say you wanna encode the probabilities sitting in a file called anc.human-mouse.probs (which was produced by prequel), using a code file called mammals.code (which was produced by pbsTrain). You'd hit it with:

pbsEncode anc.human-mouse.probs mammals.code > anc.human-mouse.bin

Look at that redirect. She's eating. 👑

🎀 OPTIONS 🎀

  • --discard-gaps, -G — throws away the gaps in the PBS 💀 The vibe here is that gaps in the input data are assumed to be represented by rows consisting of a single "-" character. So like... one lil dash, all by itself, that's a gap. That's the whole flag. Slay.
  • --help, -h — produces this help message. That's it, that's the option. Sometimes you just need a lil reassurance, and she provides it. 🫶
Lowkey important reminder: pbsEncode is the inverse of pbsDecode, so if you're out here encoding and decoding and the numbers aren't matching up, that's not a vibe check failure — that's you needing to double-check your codefile. 🙈

This has been pbsEncode version 1.4 from May 2016, serving looks in the User Commands section of the PBSENCODE(1) manual. Stay encoded, bestie. 💜✨🦋

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