TIGR-GLIMMER(1)

🎀 NAME 🎀

tigr-glimmer — the vibe is fine start/stop positions of genes in genome sequence. 💖 (Yes bestie, that's the whole name line, and yes, we're about to get into it.)

✨ SYNOPSIS ✨

tigr-extract [genome-file options]

💅 DESCRIPTION 💅

Okay so extract is the little program we're talking about here, and honestly? It does exactly what it says on the tin, no cap. It takes a FASTA format sequence file plus a file that's got a list of start/stop positions in that first file (like, the kind of thing the long-orfs program spits out) and it extracts and outputs the sequences you asked for. ✨

The first command-line argument is the name of the sequence file, and it must be in FASTA format, fr fr.

The second command-line argument is the name of the coordinate file. It's gotta contain a list of pairs of positions in the first file, one per line. The format of each entry is literally this:

<IDstring>>  <start position>  <stop position>

And like, this file should contain no other information — none, zero, nada. So if you're feeding it the output of glimmer or long-orfs, bestie you will have to cut off the header lines first. 😭 Scissors out.

The output of the program goes to standard output and has one line for each line in the coordinate file. Each line is the IDstring, then white space, then the substring of the sequence file that the coordinate pair points at. Specifically: the substring starts at the first position of the pair and ends at the second position (inclusive, so yes, that last one counts 💅). If the first position is bigger than the second, then the DNA reverse complement of each position gets generated — plot twist, but a cute one. 🦋 And start/stop pairs that "wrap around" the end of the genome? Allowed. The genome said no boundaries, only vibes. ✨

🔥 OPTIONS 🔥

• -skip — makes the output omit the first 3 characters of each sequence, aka it skips over the start codon. This was the behaviour of the previous version of the program, so if you're feeling nostalgic, this one's for you. 🫶
• -l — makes the output omit an sequences shorter than n characters. And heads up: n includes the 3 skipped characters if the -skip switch is one. 👑

👑 SEE ALSO 👑

• tigr-glimmer3 (1)
• tigr-long-orfs (1)
• tigr-adjust (1)
• tigr-anomaly (1)
• tigr-build-icm (1)
• tigr-check (1)
• tigr-codon-usage (1)
• tigr-compare-lists (1)
• tigr-extract (1)
• tigr-generate (1)
• tigr-get-len (1)
• tigr-get-putative (1)

http://www.tigr.org/software/glimmer/

Also, please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. It's giving required reading, bestie. 📚

🌸 AUTHOR 🌸

This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for the Debian system. (Not me, I just did the glow-up. 💅)

And that's a wrap on TIGR-GLIMMER(1) from the General Commands Manual, section 1 — the whole thing, no skips, no cap. Go extract some genes, you absolute icon. 🧚💜