--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_genbank2circosk.pl	Mon Jun 05 02:50:07 2023 +0000
@@ -0,0 +1,131 @@
+#!/usr/bin/perl
+#
+#       Code written by Eric Rasche
+#               mailto:rasche.eric@yandex.ru
+#               tel:404.692.2048
+#               http://eric.rasche.co.uk
+#       for
+#               Center for Phage Technology
+#
+
+use strict;
+use warnings;
+
+use CPT::GalaxyGetOpt;
+use Data::Dumper;
+
+my $ggo = CPT::GalaxyGetOpt->new();
+my %colors = map { $_ => $_ } qw(red orange yellow green blue gray black white);
+my %intensity = map { $_ => $_ } qw (vvvvl vvvl vvl vl vd vvd vvvd vvvvd);
+
+my $options = $ggo->getOptions(
+	'options' => [
+		[
+			'file',
+			'Input file',
+			{
+				required => 1,
+				validate => 'File/Input',
+				file_format => ['genbank', 'embl', 'txt'],
+			}
+		],
+		[
+			'chromosome' => 'Name for the
+			chromosome inside Circos',
+			{
+				required => 1,
+				validate => 'String'
+			}
+		],
+		[
+			'color' => 'Color to use for Circos plot',
+			{
+				required => 1,
+				validate => 'Option',
+				options  => \%colors,
+			}
+		],
+		[
+			'intensity' => 'Circos color intensity. ',
+			{
+				validate => 'Option',
+				options  => \%intensity,
+			}
+		],
+	],
+	'outputs' => [
+		[
+			'circosk',
+			'Circos Karyotype File',
+			{
+				validate       => 'File/Output',
+				required       => 1,
+				default        => 'karyotype',
+				data_format    => 'text/plain',
+				default_format => 'TXT'
+			}
+		],
+	],
+	'defaults' => [
+		'appname' => 'Genbank2CircosK',
+		'appid'   => 'Genbank2CircosK',
+		'appvers' => '1.94',
+		'appdesc' =>
+'Convert genbank files to Circos Karyotype configuration files',
+	],
+	'tests' => [
+		{
+			test_name => "Default",
+			params => {
+				'file' => 'test-data/inputs/multi.gbk',
+				'chromosome' => 'test',
+				'color' => 'red',
+				'intensity' => 'vvvl',
+			},
+			outputs => {
+				'circosk' => ['karyotype.txt', 'test-data/outputs/circosk.conf'],
+			}
+		},
+	],
+);
+
+use CPT::Bio;
+my $bio = CPT::Bio->new();
+
+my @results;
+my $c = 0;
+my $seqio = $bio->requestCopyIO( file => $options->{file} );
+
+while(my $seqobj = $seqio->next_seq()){
+	foreach my $feat ( $seqobj->get_SeqFeatures () ) {
+
+		#band test 12 CDS__test_1gbk 5715 6335 red]
+		next if ( $feat->primary_tag ne 'CDS' );
+		my $id = $bio->_getIdentifier($feat);
+		$id =~ s/\s+/_/g;
+		push(
+			@results,
+			join(
+				' ',
+				(
+					'band',
+					$options->{'chromosome'},
+					$c++,
+					$id,
+					$feat->start,
+					$feat->end,
+					(defined $options->{'intensity'} ? $options->{'intensity'} : '') . $options->{'color'}
+				)
+			)
+		);
+	}
+}
+
+my $z = join( "\n", @results );
+
+use CPT::OutputFiles;
+my $output = CPT::OutputFiles->new(
+        name => 'circosk',
+        GGO => $ggo,
+);
+$output->CRR(data => $z);