POSITIONDB(1)

💖 POSITIONDB(1) — User Commands 💖

okay bestie, pull up a chair, because we're talking about positionDB 🫶 it's a whole little program for the management of posDB files, and honestly? it's giving main character energy. it builds them, it dumps them, it tests them. a triple threat. periodt. 💅

✨ SYNOPSIS ✨

like, here's how you actually call her:

positionDB [-mersize k] [-merskip k] [-use a-b,c] [-merbegin b] [-merend
e] -sequence s.fasta -output p.posDB

positionDB -dump datafile

positionDB -test1 sequence.fasta

positionDB -test2 db.fasta sequence.fasta

four whole modes, no cap. building, dumping, and two flavours of sanity testing. pick your fighter. 🎀

🌸 OPTIONS 🌸

🦋 Building an image

this is the glow-up phase, where a posDB gets made out of your sequences. so iconic.

• -mersize k — the size of the mers. default=20. that's the k, bestie, the whole k.
• -merskip k — the skip between mers. default=0. zero skips, we're going step by step.
• -use a-b,c — specify which sequences to use. default=all. you can be picky if you want to 💅
• -merbegin b — build on a subset of the mers, starting at mer #b. default=all mers.
• -merend e — build on a subset of the mers, ending at mer #e. default=all mers.
• -sequence s.fasta — input sequences. give her the goods 🌸
• -output p.posDB — output filename. where the magic lands ✨

🎀 Dumping information about an image

• -dump datafile.posDB — spills the tea about your posDB file. just the one flag, she's lowkey mysterious like that 🙈

🧚 Running sanity tests

yes bestie, we do wellness checks on our data structures here. self care is real.

• -test1 sequence.fasta — tests if each and every mer is found in the positionDB. reports if it doesn't find a mer at the correct position. doesn't report if table has too much stuff. so it's like, thorough about missing things, but not about extras. okay girl, we see you 👀
• -test2 db.fasta sequence.fasta — builds a positionDB from db.fasta, then searches the table for each mer in sequence.fasta. reports all mers it finds.

🚨 okay so listen: This is a silly test and you shouldn't do it. that's a direct quote from the source, bestie, i'm not even joking. the manpage itself is calling it silly. don't do it. i'm begging. 😭

🌈 SEE ALSO 🌈

go bother her friends too, they're all iconic:

• existDB(1)
• meryl(1)

💜 the cute lil sign-off 💜

this whole thing is positionDB version 0~20150520+2004, and it's dated May 2015 — vintage, honestly. retro queen. she was serving before we were even online 👑

anyway ily, go build something, and remember: no skipping mers unless you mean it 🦋✨💖