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#!/usr/bin/env perl
# PODNAME: draw_bgc_maps.pl
# ABSTRACT: This script draws NRPS/PKS BGC clusters maps in PNG
# CONTRIBUTOR: Denis BAURAIN <denis.baurain@uliege.be>

use Modern::Perl '2011';
use autodie;

use Carp;
use GD::Simple;
use Getopt::Euclid qw(:vars);
use POSIX;

use Bio::Palantir;
use Bio::MUST::Core;

use aliased 'Bio::Palantir::Parser';
use aliased 'Bio::Palantir::Refiner::ClusterPlus';
use aliased 'Bio::MUST::Core::Taxonomy';
use aliased 'Bio::FastParsers::Hmmer::DomTable';


# load biosynML.xml/regions.js file report
my $report = Parser->new(
    file => $ARGV_report_file,
    module_delineation => $ARGV_module_delineation
);

my $root = $report->root;

# generate Cluster object depending on selected mode
mkdir $ARGV_outdir unless -d $ARGV_outdir;

for my $cluster ($root->all_clusters) {

    my %selection_for = (
        antismash => [$cluster],
        palantir  => [ClusterPlus->new( _cluster => $cluster,
                        module_delineation => $ARGV_module_delineation)],
        all       => [
                       $cluster, 
                       ClusterPlus->new( _cluster => $cluster,
                        module_delineation => $ARGV_module_delineation),
                       ClusterPlus->new( _cluster => $cluster, from_seq => 1,
                        module_delineation => $ARGV_module_delineation),
                     ],
    );

    
    my @clusters = @{ $selection_for{$ARGV_mode} };

    carp 'Error: the given string for --mode is not correct.'  
        . ' Only these are available: antismash, palantir, and all.' 
        unless @clusters
    ;

    map_cluster(@clusters);
}


sub map_cluster {                           ## no critic (Subroutines::ProhibitExcessComplexity)

    #TODO fix magic number
    #TODO reduce sub complexity (35)
    my @clusters = @_;