SIM2GFF(1)

📦 version 2.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 SIM2GFF 💖

okay so bestie, welcome to the sim2gff manual page — it lives in the General Commands Manual section (that's section 1, iykyk) and it's about to make your whole SIM-to-GFF pipeline slay ✨

✨ NAME ✨

sim2gff — converts SIM file into GFF formatted records 🦋

🌸 SYNOPSIS 🌸

sim2gff [-frxyHh] sim_file > gff_file

💅 DESCRIPTION 💅

okay so real talk, this manual page is just a lil brief rundown of the sim2gff command. not a whole saga, just the essentials 🎀

sim2gff is a program written in Perl (yes, Perl, she's an icon, we love her) that converts a SIM file into GFF formatted records. and why do we care?? because those records are literally made for use with gff2aplot and gff2javaplot 🔥 so if you're tryna feed those tools, this is the vibe check you needed.

🎀 OPTIONS 🎀

  • -h, --help — show summary of options. when in doubt, ask for help, no shame in it bestie 🫶
  • -f — output is written to a file named <sim_file>.gff. no more piping into the void, she's making a file 📁✨
  • -r — interchange the order of sequences (Seq1 on y-axis, Seq2 on x-axis). literally just swapping the axes, main character energy move 🔄
  • -x <name> — specify the species name for species1 (default: "Seq1"). give your girl a name 💖
  • -y <name> — specify the species name for species2 (default: "Seq2"). and give your other girl a name too 💜
  • -H — use the fasta file headers for species labels. let the fasta speak for itself, periodt 🧚

💀 EXIT STATUS 💀

the following perl-like exit status are returned — and yes, they are exactly like this, no cap:

  • 0 — Error 😭
  • 1 — Successful completion 👑
not me pointing out that 0 is the error one here — that's backwards from what your brain expects, so don't get caught slipping, fr fr.

🌈 SEE ALSO 🌈

ali2gff(1), blat2gff(1), gff2aplot(1), parseblast(1). the whole squad, go read them 🫶

👑 AUTHOR 👑

sim2gff was written by Thomas Wiehe <twiehe@imb-jena.de> 💖

this manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others). shoutout to Nelson, absolute legend 🌟

and that's the whole thing bestie, no crumbs left. this page was served up on Mon, 21 Mar 2005 21:44:15 -0300 straight from the Debian project, and honestly?? she's aged like fine wine 💅✨ mwah, go convert some SIM files 🦋

📦 where this page comes from