GFF2APLOT(1)

✨ GFF2APLOT(1) ✨ — the manual, but make it cute

okay so bestie, this is the manual page for gff2aplot, and it lives in section 1 of the General Commands Manual. Yes it's a real grown-up manpage, but we're doing this my way. Buckle up, hydrate, and let's get into it 🫶

---

🌸 NAME 🌸

gff2aplot — converting GFF files for pairwise alignments to PostScript.

like. that's the whole job description. it takes your GFF files, it makes PostScript. iconic behavior honestly 💅

---

🦋 SYNOPSIS 🦋

gff2aplot [options] <GFF_files|STDIN>

---

💖 DESCRIPTION 💖

This manual page documents briefly the gff2aplot command. (yes, briefly. it said what it said.)

gff2aplot is a program that draws color-filled alignment plots from GFF files for that alignment and two sequences annotations. so it's literally a glow-up machine for your alignment data. it draws, it colors, it fills, it serves 🌈

---

🎀 OPTIONS 🎀

A double dash on itself -- signals end of the options and start of file names (if present). You can use a single dash - as a STDIN placeholder. Available options and a short description are listed here:

• -h, --help — show summary of options. your little cheat sheet bestie.
• --version — shows current version and exits. bye 👋
• -v, --verbose — verbose mode: a full report is sent to standard error (the default is set to showing only WARNINGS). so it's chatty. main character energy.
• -V, --logs-filename <filename> — report is written to a log file.
• -q, --quiet — quiet mode, do not show any message/warning to standard error (reporting only ERRORS). it said 🤐
• -p, --page-size <format_name> — setting a page size among pre-defined ones (see below for a list of available page formats).
• --margin-left <length> — sets the left page margin.
• --margin-right <length> — sets the right page margin.
• --margin-top <length> — sets the top page margin.
• --margin-bottom <length> — sets the bottom page margin.
• -B, --background-color <color> — background color.
• -F, --foreground-color <color> — foreground color.
• -T, --title <string> — definning plot title. (their spelling, not mine, keeping it fr fr)
• -t, --subtitle <string> — definning plot subtitle.
• -X, --x-label <string> — defining X-axis label.
• -Y, --y-label <Y-Label> — defining Y-axis label.
• -L, --percent-box-label <string> — defining percent-box label.
• -l, --extra-box-label <XBox-Label> — definning Extra-Box Label.
• -x, --x-sequence-coords <pos..pos> — X-sequence coords, in <pos..pos> form.
• -S, --start-x-sequence <pos> — sets X-sequence first nucleotide.
• -E, --end-x-sequence <pos> — sets X-sequence last nucleotide.
• -y, ---y-sequence-coords <pos..pos> — Y-sequence coords, in <pos..pos> form. > ⚠️ heads up bestie: that's three dashes in ---y-sequence-coords. not a typo on my end, it's literally what the page says. copy it exactly or it will simply not slay.
• -s, --start-y-sequence <pos> — sets Y-sequence first nucleotide.
• -e, --end-y-sequence <pos> — sets Y-sequence last nucleotide.
• --x-sequence-zoom <pos..pos> — zoom coords for the X sequence.
• --y-sequence-zoom <pos..pos> — zoom coords for the Y sequence.
• -Z, --zoom [ [-S <pos>] [-E <pos>] [-s <pos>] [-e <pos>] ] — this option zooms an area you have selected with -S,-E,-s,-e (all 4 are optional).
• -z, --zoom-area [ [-S <pos>] [-E <pos>] [-s <pos>] [-e <pos>] ] — this option marks a zoom area on your plot, but does not make a zoom. it's giving "preview only", no actual follow-through 😭
• -A, --alignment-name <SeqXName:SeqYName> — defining which alignment is going to be plotted if you have more than one alignment in your gff input.
• -N, --x-sequence-name <SeqXName> — defining which sequence is going to be plotted at X-axis.
• -n, --y-sequence-name <SeqYName> — defining which sequence is going to be plotted at Y-axis.
• -r, --aplot-xy-noteq — by default X and Y axes have same length; this option disables such behaviour, so X and Y sequence will have axes-lengths proportional to their nucleotide lengths.
• -R, --xy-axes-scale <X/Y ratio> — this option allows one to set a different scale between X and Y axes lengths (by default is '1'). Below 1 values make Y larger than X, and larger than 1 result in getting X larger than Y. # Must be explained better.
• -W, --aln-scale-width — scaling score on width for Aplot lines.
• -w, --aln-scale-color — scaling score on color for Aplot lines.
• -K, --show-ribbons <ribbon_type> — force Ribbons for all features on axes to be: (N)one, (L)ines, (R)ibbons, (B)oth.
• -G, --show-grid — switches 'on' grid (default is 'off').
• -g, --hide-grid — switches 'off' grid (if switched on from customization files).
• -I, --show-percent-box — switches 'on' Percent box (default is 'off').
• -i, --hide-percent-box — switches 'off' Percent box (if set to 'on' on custom files).
• -O, --show-extra-box — switches 'on' Extra box (default is 'off').
• -o, --hide-extra-box — switches 'off' Extra box (if set to 'on' on custom files).
• -D, --aplot-box-color <color> — Aplot main box background color.
• -d, --percent-box-color <color> — Percent box background color.
• -b, --extra-box-color <color> — Extra box background color.
• --nopswarnings — switch off warnings that may appear on the final PostScript figure when X sequence, Y sequence and/or alignment input data is missing.
• -a, --hide-credits — switch off gff2aplot credits line on plot. (rude but valid 💀)
• --debug — reporting variable contents when testing the program. Requires that log report file option was also activated.
• --layout-var '<variable=value>' — layout customization variable from the command line.
• --sequence-var '<sequence::variable=value>' — sequence customization variable from the command line.
• --source-var '<source::variable=value>' — source customization variable from the command line.
• --strand-var '<strand::variable=value>' — strand customization variable from the command line.
• --group-var '<group::variable=value>' — group customization variable from the command line.
• --feature-var '<feature::variable=value>' — feature customization variable from the command line.
• -C, --custom-filename <filename> — loading customization parameters from a given file (if default .gff2aplotrc exists is loaded before it).

🌟 the margins, explained (all four of them) 🌟

Setting each page margin to <length>. If no units are provided, points are assumed. You can use points, milimeters, centimeters or inches (pt, mm, cm or in, respectively). yes, "milimeters" — one L, we don't gatekeep 🎀

🧚 the --*-var options, explained 🧚

Loading a feature/group/strand/source/sequence/layout customization variable from command-line. You can set several variables by repeating any of these options, i.e.:

... --feature-var 'cds::feature_shape=box'
    --feature-var 'cds::feature_color=blue' ...

look at you, stacking vars like a queen 👑

---

🌈 THE COLORS 🌈

Those are the colors defined in gff2aplot:

• Default Colors: black white.
• Color Palette: grey pink magenta violet blue skyblue cyan seagreen green limegreen yellow orange red brown
• You can get up to nine color shades from Variable Colors with "verydeep", "deep", "verydark", "dark", "light", "verylight", "pale" and "verypale" prefixes, as example: verydeepblue, deepblue, verydarkblue, darkblue, blue, lightblue, verylightblue, paleblue and verypaleblue.
• Dynamic colors: gradient rainbow.

🖼️ page sizes 🖼️

The following page sizes are available: from A0 to A10, from B0 to B10, 10x14, executive, folio, ledger, legal, letter, quarto, statement and tabloid.

---

💜 ENVIRONMENT VARIABLES 💜

There are two environmental variables that can be set by users to their preferences:

• You can specify the path where gff2aplot can find the default files with the shell variable "GFF2APLOT_CUSTOMPATH". Default value is the path where you are running gff2aplot.
• You can also define the default custom filename you will like with the variable "GFF2APLOT_CUSTOMFILE", program default filename for custom file is .gff2aplotrc.
• Now gff2aplot does not need to write any temporary file, so that previous versions default temporary directory path variable ("GFF2APLOT_TMP") is no longer used. rip to a real one 🪦
• Setting those vars in Bourne-shell and C-shell:
  • Using a Bourne-Shell (e.g. bash):

export GFF2APLOT_CUSTOMPATH="path"
export GFF2APLOT_CUSTOMFILE="file_name"

• Using a C-Shell:

setenv GFF2APLOT_CUSTOMPATH "path"
setenv GFF2APLOT_CUSTOMFILE "file_name"

---

👀 SEE ALSO 👀

ali2gff(1), blat2gff(1), parseblast(1), sim2gff(1).

the whole friend group, go say hi 🫶

---

👑 AUTHOR 👑

gff2aplot was written by Josep Francesc ABRIL FERRANDO <jabril@imim.es>, Thomas WIEHE <twiehe@zedat.fu-berlin.de> and Roderic GUIGO SERRA <rguigo@imim.es>.

This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others).

---

okay that's the whole page, nothing skipped, nothing dropped. go make some pretty plots bestie 💖

and that's a wrap on GFF2APLOT(1) — this version of the page is dated Mon, 21 Mar 2005 21:44:15 -0300, it's section 1 of the manual, and it ate, no crumbs left. periodt. 💅✨🦋