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lib/Bio/MUST/Drivers/Exonerate.pm  view on Meta::CPAN

package Bio::MUST::Drivers::Exonerate;
# ABSTRACT: Bio::MUST driver for running the Exonerate alignment program
$Bio::MUST::Drivers::Exonerate::VERSION = '0.252830';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Carp;
use Const::Fast;
use IPC::System::Simple qw(system);
use List::AllUtils qw(mesh);
use Module::Runtime qw(use_module);
use Path::Class qw(file);

use Bio::MUST::Core;
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::GeneticCode';
use aliased 'Bio::MUST::Core::Seq';
use aliased 'Bio::MUST::Drivers::Exonerate::Sugar';


has 'dna_seq' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Seq',
    required => 1,
);

has 'pep_seq' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Seq',
    required => 1,
);

has 'genetic_code' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::GeneticCode',
    required => 1,
);

has '_ali' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    init_arg => undef,
    writer   => '_set_ali',
    handles  => {
          all_cds =>   'all_seqs',
        count_cds => 'count_seqs',
    },
);

has '_sugars' => (
    traits   => ['Array'],
    is      => 'ro',
    isa     => 'ArrayRef[Bio::MUST::Drivers::Exonerate::Sugar]',
    default => sub { [] },
    handles  => {
        add_sugar  => 'push',
        get_sugar  => 'get',
    },
);


const my @attrs => qw(