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gff2ps - produces PostScript graphical output from GFF-files…  more info»

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GFF2PS(1)                                                  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  anno‐
       tated  features on a genomic sequence in GFF format, and pro‐
       duces 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  file‐
              name.

       -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 position 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  nu‐
              cleotide  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  permissions 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  <nao‐
       liv@gmail.com>,  for  the  Debian project (but may be used by
       others).



                   Tue, 22 Mar 2005 12:58:35 -0300         GFF2PS(1)
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