PBSDECODE(1)

✨ pbsDecode — the manual, but make it cute ✨

okay bestie, welcome to pbsDecode, section 1 of the User Commands 💅 this is literally the glow-up your encoded sequence has been waiting for.

🎀 NAME 🎀

pbsDecode — decode a binary encoding of a probabilistic biological sequence 🦋

🌸 DESCRIPTION 🌸

So here's the vibe: pbsDecode decodes a binary encoding of a probabilistic biological sequence (that's PBS for short, iykyk) 💖

It spits out a table, and the way this table works is:

• there's a row for every single position in the sequence
• there's a column for every single base
• and the (i,j)th value is the probability of base j at position i ⭐

lowkey important: you have to give it the same codefile that was used to encode the sequence. same one. no substitutions. periodt 🙈

and for the record — this program performs the inverse function of pbsEncode ✨ they're a matched set, they're iconic, they complete each other.

🧚 EXAMPLE 🧚

Decode an encoded ancestral sequence:

pbsDecode anc.human-mouse.bin mammal.code > anc.human-mouse.probs

where anc.human-mouse.bin is a binary encoding of an ancestral sequence produced by pbsEncode or prequel, and mammal.code is a codefile produced by pbsTrain. ate that whole pipeline up fr fr 💅

💖 OPTIONS 💖

• --start, -s <sidx> — decode only the subsequence starting at position <sidx>. and bestie, indexing starts with 1, not 0, we're not doing that here 🫶
• --end, -e <eidx> — decode only the subsequence ending at position <eidx>. same deal: indexing starts with 1 ⭐
• --discard-gaps, -G — do not report gaps in the PBS. gaps? not invited to this party 🚫
• --help, -h — produce this help message. your little emergency glow-up button when you forget everything 💀

🌈 SEE ALSO 🌈

ngl, the original page didn't list any SEE ALSO friends for this one, so consider this section a solo main character moment 👑

🌸 that's the whole page bestie. go decode something gorgeous. no cap.

cute little sign-off: this is pbsDecode 1.4, dated May 2016 🎀 bye lovie, drink water, read your manpages 💜✨