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

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

use autodie;
use feature qw(say);

# use Smart::Comments '###';

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

use Bio::MUST::Core;
use Bio::MUST::Core::Constants qw(:gaps);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::Seq';


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

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

# TODO: homogeneize with main class
has 'code' => (
    is       => 'ro',
    isa      => 'Str',
    default  => '1',
);

has 'model' => (
    is       => 'ro',
    isa      => 'Str',
    init_arg => undef,
    writer   => '_set_model',
);

has $_ => (
    is       => 'ro',
    isa      => 'Num',
    init_arg => undef,
    writer   => '_set_' . $_,
) for qw(
     query_start  query_end
    target_start target_end
    score
);

has $_ . '_seq' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Seq',
    init_arg => undef,
    writer   => '_set_' . $_,