Provided by: gff2aplot_2.0-8_amd64 bug


       gff2aplot - Converting GFF files for pairwise alignments to PostScript.


       gff2aplot [options] <GFF_files|STDIN>


       This manual page documents briefly the gff2aplot command.

       gff2aplot  is  a  program  that draws color-filled alignment plots from GFF files for that
       alignment and two sequences annotations.


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

       -h, --help
              Show summary of options.

              Shows current version and exits.

       -v, --verbose
              Verbose mode, a full report is sent to standard error (default is  set  to  showing
              only WARNINGS).

       -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

       -p, --page-size <format_name>
              Setting a page size among pre-defined ones see below for a list of  available  page

       --margin-left <length>

       --margin-right <length>

       --margin-top <length>

       --margin-bottom <length>
              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,

       -B, --background-color <color>
              Background color.

       -F, --foreground-color <color>
              Foreground color.

       -T, --title <string>
              Definning plot title.

       -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>

       -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>

       -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>

       --y-sequence-zoom <pos..pos>

       -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.

       -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.

              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.

              Reporting variable contents when testing the program. Requires that log report file
              option was also activated.

       --layout-var '<variable=value>'

       --sequence-var '<sequence::variable=value>'

       --source-var '<source::variable=value>'

       --strand-var '<strand::variable=value>'

       --group-var '<group::variable=value>'

       --feature-var '<feature::variable=value>'
              Loading  a  feature/group/strand/source/sequence/layout customization variable from
              command-line. You can set several variables by  repeating  any  of  these  options,
                 ... --feature-var 'cds::feature_shape=box'
                     --feature-var 'cds::feature_color=blue' ...

       -C, --custom-filename <filename>
              Loading  customization  parameters  from  a  given  file (if default ".gff2aplotrc"
              exists is loaded before it).

       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.

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


       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
        + 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.
        + Setting those vars in Bourne-shell and C-shell:
          o Using a Bourne-Shell (e.g. bash):
               export GFF2APLOT_CUSTOMPATH="path"      export GFF2APLOT_CUSTOMFILE="file_name"
          o Using a C-Shell:
               setenv GFF2APLOT_CUSTOMPATH "path"      setenv GFF2APLOT_CUSTOMFILE "file_name"


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


       gff2aplot was written by Josep Francesc  ABRIL  FERRANDO  <>,  Thomas  WIEHE
       <> and Roderic GUIGO SERRA <>.

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

                                 Mon, 21 Mar 2005 21:44:15 -0300                     GFF2APLOT(1)