EDAMCLEAN(1e)

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

💖 EDAMCLEAN 💖 (that's the 1e manual, bestie — EMBOSS Manual for Debian, we're in the Debian EMBOSS zone)

✨ NAME ✨

edamclean — validate and fix EDAM OBO ontology. yes literally that's the whole job and she's iconic for it 💅

🌸 SYNOPSIS 🌸

edamclean -edaminfile infile -taxdirectory directory -mode selection
          -edamoutfile outfile -logfile outfile -xmlfile outfile
          -xmloutdir outdir

edamclean -help

okay so that's a LOT of flags but we're gonna go through every single one, no skipping, no cap 🫶

🦋 DESCRIPTION 🦋

edamclean is a command line program from EMBOSS — and if you don't know, EMBOSS is "the European Molecular Biology Open Software Suite" 💖. She's part of the "Ontology:EDAM" command group(s), so she runs with a very specific little friend group, iykyk.

🎀 OPTIONS 🎀

💜 Input section

  • -edaminfile infile — the EDAM OBO file she reads in. Default value: /homes/jison/edam/EDAM.obo (yes that is a real default path, we don't question it, we respect it)
  • -taxdirectory directory — points at the taxonomy directory 🌈

⭐ Required section

  • -mode selection — required bestie, don't skip her. Default value: Report only

🔥 Advanced section

(this section is genuinely empty in the original — nothing here, she's just vibing 💀)

💅 Output section

  • -edamoutfile outfile — where the cleaned-up EDAM output goes. Default value: EDAM_out.obo
  • -logfile outfile — the log file. Default value: EDAM_out.log
  • -xmlfile outfile — the XML output file. Default value: EDAM_out.xml
  • -xmloutdir outdir — the directory for the XML output 🧚

😭 BUGS 😭

Found a bug? Not her fault, she's doing her best 🙈 Report it to the Debian Bug Tracking system at http://bugs.debian.org/emboss, or go straight to the EMBOSS developers at http://sourceforge.net/tracker/?group_id=93650&atid=605031. Tell them the vibe check failed, they'll know.

👑 SEE ALSO 👑

edamclean is fully documented via the tfm(1) system. go read that too, she's thorough like that.

💖 AUTHOR 💖

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

  • Wrote the script used to autogenerate this manual page. (the script ate, 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. periodt.

✨ and that's the whole page bestie ✨ — this was EMBOSS 6.4.0, dated 05/11/2012, and you just read the EDAMCLEAN(1e) manual like a legend 🫶💜 go validate some ontology, you've got this 👑

📦 where this page comes from