gff2ps(1)
NAME
gff2ps - Produces PostScript graphical output from GFF-files.
SYNOPSIS
gff2ps [options] -- gff_files
DESCRIPTION
This program draws color-filled DotPlots from files with gff-formatted
data fields. The program takes as input the annotated features on a
genomic sequence in GFF format, and produces a visual output in
PostScript.
OPTIONS
-h Show summary of options.
- -H <option>
- Shows only help for the especified option.
- -V Verbose mode, a full report is sent to standard error (default
- only sends Warnings).
- -v Silent mode: Disable all warnings, no messages sent to standard
- error.
- -d Write (or rewrite if exists) default customfile.
- -D <default_custom_filename>
- Create a new default customfile with the given filename.
- -C <custom_filename>
- Load given custom file and append to default custom file (.gff2psrc).
- -s <page_size>
- Useful to modify page size (default is a4).
- -p Switches page orientation to Portrait (default is Landscape).
- -G <color_name>
- Sets color for FOREGROUND (default is black).
- -g <color_name>
- Sets 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 posi
- tion from input gff-files).
- -b Blocks from left to right and from top to bottom (default is top
- to bottom first).
- -L Switch off Header (Title area).
- -T <title_string>
- Defining title (default is input gff filename).
- -t <subtitle_string>
- Defining 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 color for frame "0" (default is blue).
- -1 Sets color for frame "1" (default is red).
- -2 Sets color for frame "2" (default is green).
- -3 Sets color for frame "." (default is orange).
- -n Switch off labels for element positions.
- -a Switch off CopyRight line on plot.
ENVIRONMENT VARIABLES
- There are three environmental variables that can be set by users to
their pre ferences:
- + You can specify the path where GFF2PS can find the default files
- with the shell variable "GFF2PS_CFDIR". Default value is path where you are running GFF2PS.
- + You can also define the default custom filename you will like with
- the variable "GFF2PS_CUSTOMFILE", program default filename for custom file is ".gff2psrc".
- + GFF2PS needs to write few temporary files in a directory with per
- missions for current user to read and write. 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"
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 "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.
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).