ABIVIEW(1e)

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

💖 ABIVIEW — bestie, it's giving sequencer tea 💖

okay so this one lives in the EMBOSS Manual for Debian (that's the man page section 1e for anyone keeping score), and it's literally about peeking at the trace inside an ABI sequencer file. no cap.

✨ NAME ✨

abiview — Display the trace in an ABI sequencer file

🌈 SYNOPSIS 🌈

abiview -infile infile -outseq seqout -graph xygraph
        [-startbase integer] [-endbase integer] -separate boolean
        [-yticks boolean] [-sequence boolean] [-window integer]
        [-bases string]

abiview -help

like, that's the whole vibe. -infile, -outseq, -graph and -separate are the ones you have to bring to the party, the rest are optional besties. and there's always -help if you're lost (you're not, but still). 🫶

🦋 DESCRIPTION 🦋

abiview is a command line program straight outta EMBOSS — "the European Molecular Biology Open Software Suite" (iconic name, iconic suite). it hangs out in the "Data retrieval:Sequence data,Display" command group(s), so basically it's the girl who fetches your sequence data and makes it cute to look at. main character energy fr fr. 💅

🎀 OPTIONS 🎀

💜 Input section

  • -infile infile — the file you're feeding in. your ABI sequencer file, the one with the tea in it.

🌸 Output section

  • -outseq seqout — where the sequence goes when you write it out.
  • -graph xygraph — the graph output. yes, a whole xygraph, because we're visual girls.
  • -startbase integer — first sequence base to report or display. where the story begins.
  • -endbase integer — Last sequence base to report or display. If the default is set to zero then the value of this is taken as the maximum number of bases. so like, 0 means "girl, just go all the way to the end". 🏁
  • -separate boolean — Default value: N
  • -yticks boolean — Default value: N
  • -sequence boolean — Default value: Y
  • -window integer — Default value: 40
  • -bases string — Default value: GATC
lowkey notice how -separate, -yticks, -sequence, -window and -bases all come with defaults baked in, while -startbase and -endbase are the free spirits with no default listed. don't come for me, that's just what the page says. 🙈

💀 BUGS 💀

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).

like, if something's broken, tell the Debian folks or the EMBOSS devs directly. they wanna know, fr. 🐛

⭐ SEE ALSO ⭐

abiview is fully documented via the tfm(1) system. so if you want the full lore, that's where it's at. iykyk. 📖

👑 AUTHOR 👑

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

  • Wrote the script used to autogenerate this manual page.

so yes, the manual page itself was autogenerated by a script. the girls were automating even back then. slay. 💖

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.

and that's the whole page, bestie — no notes, no skips, every single option accounted for. this lil icon of a man page comes to you from EMBOSS 6.4.0, dated 05/11/2012. periodt. 💅✨🎀

📦 where this page comes from