circos 0.64-1 / usr / bin / circos

#!/usr/bin/env perl

=pod

=head1 NAME

                                    ____ _
                                   / ___(_)_ __ ___ ___  ___
                                  | |   | | '__/ __/ _ \/ __|
                                  | |___| | | | (_| (_) \__ \
                                   \____|_|_|  \___\___/|___/

                                                round is good

circos - generate circularly composited information graphics

=head1 SYNOPSIS

  circos -conf circos.conf [-silent] [-help] [-man]

  # detailed debugging for code components
  # see http://www.circos.ca/documentation/tutorials/configuration/debugging
  circos -debug_group GROUP1,[GROUP2,...]

  # configuration dump
  circos -cdump [BLOCK1/[BLOCK2/...]]

  # overriding configuration parameters
  circos -param image/radius=2000p -param ideogram/show=no

=head1 DESCRIPTION

Circos is a software package for visualizing data and information. It
visualizes data in a circular layout, which makes Circos ideal for
exploring relationships between objects or positions. There are other
reasons why a circular layout is advantageous, not the least being the
fact that it is attractive.

Circos is ideal for creating publication-quality infographics and
illustrations with a high data-to-ink ratio, richly layered data and
pleasant symmetries. You have fine control each element in the figure
to tailor its focus points and detail to your audience.

=head1 CONFIGURATION

Settings are meant to be passed using a plain-text configuration
file. This file can be created manually or by another script, which
allows Circos to be fully automated.

For full documentation, see

  L<http://www.circos.ca/documentation/tutorials>

=head2 Syntax

Configuration is plain-text and composed of hierarchical blocks. Some
blocks, such as C<<ideogram>> are mandatory, while others like
C<<backgrounds>> are optional. 

To get started, refer to the quick guide tutorial.

  L<http://www.circos.ca/documentation/tutorials/quick_guide>

A typical configuration file might look like this

  # image size and format 
  <image>
   ...
  </image>
 
  # position and size of ideograms
  <ideogram>
   ...
  </ideogram>

  # position, type and format of data tracks
  <plots>
   <plot>
     ...
   </plot>
   ...
  </plots>

  # colors, fonts and fill patterns
  <<include /usr/share/circos/etc/colors_fonts_patterns.conf>>

  # system parameters
  <<include /usr/share/circos/etc/housekeeping.conf>>

=head2 Modularity

The C<<<include FILE>>> directive imports one configuration file into another. This facility helps to keep configuration files modular.

Parameter definitions that do not frequently change, such as color and font definitions, are conventionally imported from files found in F<etc/> in the distribution.

In the tutorials, you'll find that the C<<ideogram>> and C<<ticks>> blocks are imported into the main configuration file. Because these blocks can get quite large, the main configuration file is more legible if they are relegated to separate files.

=head2 Overriding with *

To override a parameter that has been included from a file, use the C<*> suffix. The suffix is required because multiple definitions of a parameter are not allowed, except in cases where a parameter is may have more than one value.

  <image>
  # included file defines 'radius'
  <<include /usr/share/circos/etc/image.conf>>
  # this will override the radius value
  radius* = 2500p
  </image>

The C<*> suffix can be repeated to specify which value takes precedence in a block.

  radius = 1500p
  radius* = 2500p
  radius** = 3000p # this instance of radius will be used

=head2 Overriding with Command Line

Any configuration parameter in a unique block name can be specified on
the command line using

  -param PATH/PARAM=value

For example,

  # <ideogram>
  #   show = no
  #   ...
  # </ideogram>
  -param ideogram/show=no

  # <ideogram>
  #   <spacing>
  #     default = 0.01r
  #   </spacing>
  #   ...
  # </ideogram>
  -param ideogram/spacing/default=0.01r

Multiple parameters can be redefined, each with its own C<-param> flag

  -param show_ticks=no -param image/radius=2000p

=head2 Merging Blocks

Multiple instances of the following blocks are automatically merged: C<<ideogram>>, C<<colors>>, C<<fonts>>, C<<paterns>>, C<<image>>, C<<links>>, C<<plots>> and C<<highlights>>.

The purpose of this is to allow you to add to canonical definitions.

  # this file defines default <colors>, <fonts> and <patterns>
  <<include /usr/share/circos/etc/colors_fonts_patterns.conf>>

  # add to the colors block
  <colors>
  mycolor = 150,25,25
  </colors>

=head1 OPTIONS

=head2 Configuration

=over

=item -configfile FILE

Name of configuration file. This is required.

Circos will attempt to guess the location of this file, searching for
C<circos.conf> in C<.>, C<..>, and C<../..>.

=back

=head2 Output Format

=over

=item -png, -nopng

=item -svg, -nosvg

Toggles output of PNG and SVG files.

=back

=head2 Output Paths

=over 

=item -outputdir DIR

=item -outputfile FILE

Change the output directory and filename.

=back 

=head2 Debugging

=over

=item -debug LEVEL

Turn on debugging output.

=item -debug_group GROUP1,[GROUP2,...]

Turn on debugging output for specific groups. For a list of groups, see

  L<http://www.circos.ca/documentation/tutorials/configuration/debugging>

=item -silent 

Generate no reporting.

=back

=head2 Usage

=over

=item -version

Show the version.

=item -help

Show brief usage synopsis.

=item -man

Show man page.

=back

=cut

use strict;
use warnings;
use FindBin;
use Getopt::Long;
use Pod::Usage;

use lib "$FindBin::RealBin";
use lib "$FindBin::RealBin/../lib";
use lib "$FindBin::RealBin/lib";
use Circos;

use Circos::Debug;

my %OPT;
GetOptions(\%OPT,
					 'configfile=s',
					 'param=s@',
					 'cdump:s',
					 'cdebug',

					 'outputdir=s',
					 'outputfile=s',
					 'png!',
					 'svg!',
					 'imagemap',

					 'color_cache_rebuild',
					 'color_cache_static',
					 'randomcolor:s',

					 'help',
					 'man',
					 'silent',
					 'paranoid!',
					 'warnings!',
					 'fakeerror=s',
					 'debug+',
					 'debug_group=s',
					 'version',

					 'show_ticks!',
					 'show_tick_labels!',

#	   'chromosomes=s',
#	   'chromosomes_display_default!',
#	   'chromosomes_order=s',
#	   'chromosomes_scale=s',
#	   'chromosomes_radius=s',
#	   'usertext1=s',
#	   'usertext2=s',
#	   'usertext3=s',
#	   'usertext4=s',
#	   'tagname',
#	   'file_delim=s',
#	   'background=s',
#	   'image_map_name=s',
#	   'image_map_file=s',
#	   'image_map_use',
#	   'image_map_missing_parameter',

	  );

pod2usage()            if $OPT{'help'};
pod2usage(-verbose=>2) if $OPT{'man'};
#$OPT{debug_group} .= "conf" if $OPT{cdebug};
Circos->run(%OPT);

# -------------------------------------------------------------------

=pod

=head1 AUTHOR

Martin Krzywinski L<martink@bcgsc.ca> L<http://mkweb.bcgsc.ca>

=head1 RESOURCES

L<http://www.circos.ca>

=head1 CITING

If you are using Circos in a publication, please cite as

Krzywinski, M., J. Schein, I. Birol, J. Connors, R. Gascoyne,
D. Horsman, S. Jones, and M. Marra. 2009. Circos: an Information
Aesthetic for Comparative Genomics. Genome Res 19:1639-1645.

=head1 CONTRIBUTORS

Ken Youens-Clark L<kyclark@gmail.com>

=head1 SEE ALSO

Hive plots L<http://www.hiveplot.com>

=head1 COPYRIGHT & LICENSE

Copyright 2004-2012 Martin Krzywinski, all rights reserved.

This file is part of the Genome Sciences Centre Perl code base.

This script is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This script is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this script; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

=cut