GFF2PS(1)

💅 GFF2PS(1) — like, the manual, but make it make sense

okay bestie, sit down, hydrate, and let me tell you about gff2ps, which lives in section 1 of the manual pages (that's the General Commands Manual, iykyk) ✨

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🌸 NAME 🌸

gff2ps — the way it produces PostScript graphical output from GFF-files. that's it, that's the whole vibe. periodt. 💅

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🎀 SYNOPSIS 🎀

gff2ps [options] -- gff_files

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🦋 DESCRIPTION 🦋

so this program draws color-filled DotPlots from files that have gff-formatted data fields. it takes the annotated features on a genomic sequence in GFF format as its input, and it gives you back a visual output in PostScript. it's giving "turn your boring text annotations into art" and honestly? iconic. 🌈

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✨ OPTIONS ✨

here's the whole menu, no skips, no skimming, we read every single one 🫶

• -h — show a summary of options. the lil recap, the tl;dr 💖
• -H <option> — shows only help for the especified option. just that one. no extras. ✨
• -V — Verbose mode: a full report is sent to standard error (by default only Warnings get sent). she's chatty, she's telling you everything 💬
• -v — Silent mode: disable all warnings, no messages sent to standard error. not a single peep. 🤫
• -d — write (or rewrite, if it already exists) the default customfile.
• -D <default_custom_filename> — create a brand new default customfile with the given filename. new name, who dis 🎀
• -C <custom_filename> — load the given custom file and append it to the default custom file (.gff2psrc).
• -s <page_size> — useful to modify page size (default is a4). 📄
• -p — switches page orientation to Portrait (default is Landscape). she turned around 💅
• -G <color_name> — sets the color for FOREGROUND (default is black).
• -g <color_name> — sets the color for BACKGROUND (default is white).
• -P <#> — sets how many pages are needed to split your output (default is one).
• -S <#> — zoom first nucleotide (default is sequence origin).
• -E <#> — zoom last nucleotide (default is sequence length).
• -B <#> — sets blocks per page (default is one).
• -N <#> — sets nucleotides per line (default is the largest sequence position from input gff-files).
• -b — blocks go from left to right and from top to bottom (default is top to bottom first). choose your reading order, main character 🧚
• -L — switch off the Header (Title area).
• -T <title_string> — defining the title (default is input gff filename).
• -t <subtitle_string> — defining the subtitle (default is none).
• -l — does not show page numbering.
• -O — does not show date.
• -o — does not show time.
• -M <#> — number of major tickmarks per line (default 10).
• -K <#> — major tickmarks scale in nucleotides; default is nucleotide length for lines divided by major tickmarks number (see option -T).
• -m <#> — number of minor tickmarks between major tickmarks (default 10).
• -k <#> — minor tickmarks scale in nucleotides; default is major tickmarks size divided by minor tickmarks number (see option -t).
• -w, -f — switch off displaying forward-strand (Watson) elements.
• -c, -r — switch off displaying reverse-strand (Crick) elements.
• -i — switch off displaying strand-independent elements.
• -0 <color_name> — sets the color for frame "0" (default is blue).
• -1 — sets the color for frame "1" (default is red).
• -2 — sets the color for frame "2" (default is green).
• -3 — sets the color for frame "." (default is orange).
• -n — switch off labels for element positions.
• -a — switch off the CopyRight line on the plot.

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💜 ENVIRONMENT VARIABLES 💜

there are three environmental variables that you, yes you, can set to your pre ferences:

• you can specify the path where GFF2PS can find the default files with the shell variable GFF2PS_CFDIR. default value is the path where you are running GFF2PS.
• you can also define the default custom filename you will like with the variable GFF2PS_CUSTOMFILE; the program's default filename for the custom file is .gff2psrc.
• GFF2PS needs to write a few temporary files in a directory with permissions for the current user to read and write. the default temporary directory path is set to /tmp/, but you can assign a different temporary directory path using the variable GFF2PS_TMP.

🐚 setting those vars in Bourne-shell (bash):

export GFF2PS_CFDIR="path"
export GFF2PS_CUSTOMFILE="file_name"
export GFF2PS_TMP="path"

🐚 using a C-Shell (csh):

setenv GFF2PS_CFDIR "path"
setenv GFF2PS_CUSTOMFILE "file_name"
setenv GFF2PS_TMP "path"

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🌟 COMMENTS 🌟

• colors defined are:

Basic Colors: black white

Variable Colors: grey magenta violet blue skyblue cyan seagreen green lime green yellow orange red brown

you can get five color shades from Variable Colors with the "verydark", "dark", "light" and "verylight" prefixes. an example: verydarkseagreen darkseagreen seagreen lightseagreen verylightseagreen ✨

• page Sizes defined are:

from A0 to A10, from B0 to B10, 10x14, executive, folio, ledger, legal, letter, quarto, statement and tabloid.

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👑 AUTHOR 👑

gff2ps was written by Josep Francesc ABRIL FERRANDO <jabril@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). 🫶

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and that's the whole page bestie!! written up on Tue, 22 Mar 2005 12:58:35 -0300 and stamped onto the GFF2PS(1) page itself. go make some DotPlots, you absolute icon 💖🌸🦋