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lib/Bio/MUST/Core/GeneticCode/Factory.pm  view on Meta::CPAN

package Bio::MUST::Core::GeneticCode::Factory;
# ABSTRACT: Genetic code factory based on NCBI gc.prt file
$Bio::MUST::Core::GeneticCode::Factory::VERSION = '0.252040';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use autodie;
use feature qw(say);

use Carp;
use Const::Fast;
use File::Spec;
use List::AllUtils qw(uniq);
use LWP::Simple qw(get);
use Path::Class qw(file);
use Try::Tiny;

use Bio::MUST::Core::Types;
use aliased 'Bio::MUST::Core::GeneticCode';


# public path to NCBI Taxonomy dump directory
has 'tax_dir' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Types::Dir',
    coerce   => 1,
);


# private hash hosting NCBI codes
has '_code_for' => (
    traits   => ['Hash'],
    is       => 'ro',
    isa      => 'HashRef[Bio::MUST::Core::GeneticCode]',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_code_for',
    handles  => {
             code_for => 'get',
        list_codes    => 'keys',
    },
);


## no critic (ProhibitUnusedPrivateSubroutines)

sub _build_code_for {
    my $self = shift;

    # split file content into code blocks
    my @codes = $self->_get_gcprt_content =~ m/ \{ ( [^{}]+ ) \} /xmsgc;
    croak "[BMC] Error: cannot parse 'gc.prt' file; aborting!" unless @codes;

# Genetic-code-table ::= {
# ...
#  {
#     name "Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate
#  Mitochondrial; Mycoplasma; Spiroplasma" ,
#   name "SGC3" ,
#   id 4 ,
#   ncbieaa  "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
#   sncbieaa "--MM---------------M------------MMMM---------------M------------"
#   -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG