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       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 ERRORS).

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

       --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, respectively).

       -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

       -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 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.

              Loading       a      feature/group/strand/source/sequence/layout
              customization variable from command-line. You  can  set  several
              variables by repeating any of these options, i.e.:
                 ... --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
        + 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 gff2aplot.
        + 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
          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