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CircosAPI v0.6 beta

APIs for CIRCOS: Circular Genome Data Visualization

Requirements

  1. Perl > 5.12
  2. Moose
  3. JSON::PP
  4. String::Util

Features

  • Programmatically generate your Circos graphics via Perl
  • Configure your own defaults for your pipelines via JSON

Note: This module is not a syntax checker. You need to know how CIRCOS works.

Getting Started

In your script.pl

#!/usr/bin/perl
use lib::CircosAPI;
my $c = CircosAPI->new();

By instantiating a new instance of CircosAPI without any parameters will fill the minimal required parameters based on the defaults.json as found in defaults directory. You can change the defaults using a JSON file or pass a Hash to the blocks (shown below).

my $b = Base->new(karyotype => 'hg19');
my $id = Ideogram->new(radius => '0.95r', thickness => '20p');
my $c = CircosAPI->new(base => $b, ideogram => $id);
print $c->compile;

In your shell

$ perl script.pl > circos.conf
$ circos -conf circos.conf

Please read the API reference for more details on the parameters that you need to provide and the default value for some of the parameters if you do not provide them.