PRETTYPLOT(1e)

💖 PRETTYPLOT(1e) — the EMBOSS Manual for Debian glow-up 💖

okay bestie, sit down, hydrate, because this is prettyplot(1e) and she is serving sequence alignments with pretty formatting. this page lives in the EMBOSS Manual for Debian, and it's gonna be so good. no cap. 🦋

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🌸 NAME 🌸

prettyplot — Draw a sequence alignment with pretty formatting

like... the name literally ate. she draws alignments. prettily. periodt. 💅

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✨ SYNOPSIS ✨

prettyplot -sequences seqset [-matrixfile matrix]
           [-residuesperline integer] [-resbreak integer]
           [-ccolours boolean] [-cidentity string] [-csimilarity string]
           [-cother string] [-docolour boolean] [-shade string]
           [-pair array] [-identity integer] [-box boolean]
           [-boxcol boolean] [-boxuse string] [-name boolean]
           [-maxnamelen integer] [-number boolean]
           [-listoptions boolean] [-plurality float]
           [-consensus boolean] [-collision boolean] [-alternative list]
           [-showscore integer] [-portrait boolean] -graph graph

prettyplot -help

see how -sequences and -graph are the only ones with no brackets?? that means they're required, bestie. everything else is optional because she's flexible like that. and yes, prettyplot -help is a whole vibe of its own. 🫶

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👑 DESCRIPTION 👑

so prettyplot is a command line program from EMBOSS, which is short for “the European Molecular Biology Open Software Suite” (iconic name, honestly). she's part of the "Alignment:Multiple,Display" command group(s) — which is exactly the little squad you'd expect her to run with. 🌈

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🎀 OPTIONS 🎀

okay so this is the long part. do NOT skip. every single flag is here and she deserves your attention. 💖

💜 Input section 💜

• -sequences seqset — the sequences you're feeding her. this one's a need, not a want. ✨
• -matrixfile matrix — this is 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 chillin' in the 'data' directory of your EMBOSS installation. 🍓

🌸 Additional section 🌸

• -residuesperline integer — the number of residues to be displayed on each line. Default value: 50
• -resbreak integer — Default value: $(residuesperline)
• -ccolours boolean — Default value: Y
• -cidentity string — Default value: RED
• -csimilarity string — Default value: GREEN
• -cother string — Default value: BLACK
• -docolour boolean — Default value: N
• -shade string — set to BPLW for normal shading (black, pale, light, white). so for pair = 1.5,1.0,0.5 and shade = BPLW:
  • Residues score 1.5 or over ... BLACK (B)
  • 1.0 to 1.5 ... BROWN (P)
  • 0.5 to 1.0 ... WHEAT (L)
  • under 0.5 .... WHITE (W)

the only four letters allowed are BPLW, in any order. that's it, that's the rule. 💀

• -pair array — Default value: 1.5,1.0,0.5
• -identity integer — (no default, no description, she's mysterious like that 🙈)
• -box boolean — Default value: Y
• -boxcol boolean — Default value: N
• -boxuse string — Default value: GREY
• -name boolean — Default value: Y
• -maxnamelen integer — Default value: 10
• -number boolean — Default value: Y
• -listoptions boolean — Default value: Y
• -plurality float — Default value: @( $(sequences.totweight) / 2)

🧚 Consensus section 🧚

• -consensus boolean — Default value: N
• -collision boolean — Default value: Y
• -alternative list — the values are, and we're quoting her exactly because precision is everything:
  • 0 : Normal collision check. (default)
  • 1 : Compares identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred.
  • 2 : If another residue has a greater than or equal to matching score and these do not match then a collision has occurred.
  • 3 : Checks all those not in the current consensus. If any of these give a top score for matching or identical scores then a collision has occured.

(yes, "occured" — we're keeping her typo, it's canon, it's part of the lore now 🫶)

• -showscore integer — Default value: -1
• -portrait boolean — Default value: N

🌟 Output section 🌟

• -graph graph — the output graph. also required. she needs to know where to put the masterpiece. 🔥

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💀 BUGS 💀

not me having to tell you this, but if you find a bug, 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. they'll fix it, bestie, don't stress. 💅

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🦋 SEE ALSO 🦋

prettyplot is fully documented via the tfm(1) system. so if you need more, that's where the lore lives. ✨

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🌈 AUTHOR 🌈

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

• Wrote the script used to autogenerate this manual page.

(thank you for your service, legends 🫡)

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💖 COPYRIGHT 💖

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.

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and that's the whole page, bestie!! 🎀 this gorgeous thing is EMBOSS 6.4.0, dated 05/11/2012, and she's still out here drawing pretty alignments like the main character she is. go make something beautiful with her. slay. 👑✨💅