CONS(1e)

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

💖 CONS(1e) — the manual page, but make it make sense 💖

okay bestie, this is page CONS(1e) from the EMBOSS Manual for Debian, and we're gonna get you fluent in cons in like five minutes. no cap. ✨

🌸 NAME 🌸

cons — create a consensus sequence from a multiple alignment. that's it, that's the whole job, and it does it beautifully. 💅

🎀 SYNOPSIS 🎀

cons -sequence seqset [-datafile matrix] [-plurality float]
     [-identity integer] [-setcase float] -outseq seqout [-name string]

cons -help

the ones in brackets are optional, the ones without are mandatory, so -sequence and -outseq are the main characters here. 👑

🦋 DESCRIPTION 🦋

cons is a command line program from EMBOSS (that's "the European Molecular Biology Open Software Suite", iykyk) and it lives in the "Alignment:Consensus" command group(s). so yeah, it takes your alignment and gives you the group chat's collective opinion as one sequence. 🫶

✨ OPTIONS ✨

💜 Input section

  • -sequence seqset — the file containing a sequence alignment. this is your raw material, your source text, your group chat history. don't skip it. 💖
  • -datafile matrix — the scoring matrix file used when comparing sequences. by default it's the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). you'll find these files in the 'data' directory of your EMBOSS installation. so like, they're already there, bestie, you don't gotta hunt. 🌈

🌸 Additional section

  • -plurality float — sets a cut-off for the number of positive matches below which there is no consensus. the default plurality is taken as half the total weight of all the sequences in the alignment. Default value: @( $(sequence.totweight) / 2) ✨
  • -identity integer — lets you set the required number of identities at a site for it to give a consensus at that position. so if you set this to the number of sequences in the alignment, only columns of identities contribute to the consensus. strict queen energy. 👑
  • -setcase float — sets the threshold for the positive matches above which the consensus is upper-case and below which the consensus is in lower-case. Default value: @( $(sequence.totweight) / 2) 💅

🎀 Output section

  • -outseq seqout — the output sequence file. your consensus goes here. 🌟
  • -name string — a name. for the thing. yep, that's the description we got, and we're keeping it fr fr. 🍓

💀 BUGS 💀

found a bug? (rude of it, honestly.) report it 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). they'll handle it. 🙈

🧚 SEE ALSO 🧚

cons is fully documented via the tfm(1) system. go read that if you want the deep lore. 📖

🌟 AUTHOR 🌟

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

  • Wrote the script used to autogenerate this manual page. iconic behavior, honestly. 🫶

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 like, keep the license terms intact if you're passing this around, bestie — that part is not optional. 💜

and that's the whole vibe check, babe — page CONS(1e), from EMBOSS 6.4.0, dated 05/11/2012. go build something slay. 🦋✨🎀

📦 where this page comes from