Man Linux: Main Page and Category List


       gff2ps - Produces PostScript graphical output from GFF-files.


       gff2ps [options] -- gff_files


       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


       -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

       -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

       -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

       -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  nucleotide
              length  for  lines divided by major tickmarks number (see option

       -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.


       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"


       * 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.


       gff2ps was written by Josep Francesc ABRIL FERRANDO <>.

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

                        Tue, 22 Mar 2005 12:58:35 -0300