TCODE(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 TCODE(1e) — the EMBOSS Manual for Debian, but make it a group chat 💖

okay bestie so you opened the tcode manual page on a Debian box and it's giving very "written by a bot in 2012" energy, so let me translate the whole thing for you. no cap, every single detail is still here. 🫶

✨ NAME ✨

tcode — identify protein-coding regions using the Fickett TESTCODE statistic 🌸

like, it looks at your sequence and goes "mm, this bit codes for protein, this bit doesn't." iconic.

🎀 SYNOPSIS 🎀

tcode -sequence seqall -datafile datafile -window integer -step integer
      -plot toggle -outfile report -graph xygraph

tcode -help

that's the whole vibe. run it with those flags, or run tcode -help if you just wanna be handheld. 💅

🌈 DESCRIPTION 🌈

so tcode is a command line program from EMBOSS — that's "the European Molecular Biology Open Software Suite", the full government name, periodt — and it lives in the "Nucleic:Gene finding" command group(s). it's a gene-finding girlie. it's out here hunting coding regions and it does not need a GUI to do it. 💜

⭐ OPTIONS ⭐

🦋 Input section 🦋

  • -sequence seqall — your sequence goes here, bestie. the input. the moment. ✨
  • -datafile datafile — the default data file is Etcode.dat and it contains coding probabilities for each base. and not just one flavour — the probabilities are for both positional and compositional information. Default value: Etcode.dat

👑 Required section 👑

  • -window integer — this is the number of nucleotide bases over which the TESTCODE statistic will be performed each time. then the window slides along the sequence, covering the same number of bases each time. it's a sliding window, she's a main character. Default value: 200

🧚 Advanced section 🧚

  • -step integer — the selected window will, by default, slide along the nucleotide sequence by three bases at a time, retaining the frame (although the algorithm is not frame sensitive — just so you know, it's giving frame-retaining but not frame-dependent, iykyk). you can alter this to increase or decrease the increment of the slide. Default value: 3

💖 Output section 💖

  • -plot toggle — on selection, a graph of the sequence (X axis) plotted against the coding score (Y axis) will be displayed. sequence above the green line is coding, and sequence below the red line is non-coding. Default value: N
  • -outfile report — the file your report lands in. 🍓
  • -graph xygraph — the file your graph lands in. 📈

💀 BUGS 💀

found a bug? not the vibe, but ok, report it. bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). tell them exactly what happened, they will handle it. 🙈

🔥 SEE ALSO 🔥

tcode is fully documented via the tfm(1) system. so if you want the deep lore, that's where it's at. ⭐

🌸 AUTHOR 🌸

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • wrote the script used to autogenerate this manual page. yeah, a script wrote this. we been knew. 💅

this manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. it can be redistributed under the same terms as EMBOSS itself. so, same energy as EMBOSS, copy it accordingly, no stealing without the terms. 🫶

fr fr, that's the whole page. nothing skipped, nothing invented, everything exactly where it was.

and that's a wrap, bestie — this page is from EMBOSS 6.4.0, dated 05/11/2012, and it's the TCODE(1e) manual. slay. 💖✨🎀

📦 where this page comes from