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lib/Bio/AutomatedAnnotation/CommandLine/ParseGenesFromGFFs.pm  view on Meta::CPAN

package Bio::AutomatedAnnotation::CommandLine::ParseGenesFromGFFs;
$Bio::AutomatedAnnotation::CommandLine::ParseGenesFromGFFs::VERSION = '1.182770';
# ABSTRACT: provide a commandline interface to pull out genes from multiple GFF files


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Bio::AutomatedAnnotation::ParseGenesFromGFFs;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'help'        => ( is => 'rw', isa => 'Bool',     default  => 0 );

has 'amino_acids'       => ( is => 'rw', isa => 'Bool', default => 0);
has 'gff_files'         => ( is => 'rw', isa => 'ArrayRef' );
has 'search_query'      => ( is => 'rw', isa => 'Str' );
has 'search_qualifiers' => ( is => 'rw', isa => 'ArrayRef', default => sub { ['gene'] } );
has 'output_filename'   => ( is => 'rw', isa => 'Str' );

has '_error_message'    => ( is => 'rw', isa => 'Str' );

sub BUILD {
    my ($self) = @_;

    my (
        $nucleotides,       $gff_files,            $search_query, $search_qualifiers, $output_filename,        $help
    );

    GetOptionsFromArray(
        $self->args,
        'g|gene=s'          => \$search_query,
        'p|search_products' => \$search_qualifiers,
        'o|output=s'        => \$output_filename,
        'n|nucleotides'     => \$nucleotides,
        'h|help'            => \$help,
    );

    if(defined($nucleotides))
    {
      $self->amino_acids(0);
    }
    else
    {
      $self->amino_acids(1);
    }
    
    if(defined($search_query))
    {
      $self->search_query($search_query);
    }
    else
    {
      $self->_error_message("Error: You must provide a gene to search for");
    }
    
    $self->output_filename($output_filename) if(defined($output_filename));
    push(@{$self->search_qualifiers}, 'product') if(defined($search_qualifiers));

    if(@{$self->args} == 0)
    {
      $self->_error_message("Error: You need to provide at least 1 GFF file");
    }

    for my $filename (@{$self->args})
    {
      if(! -e $filename)
      {
        $self->_error_message("Error: Cant access file $filename");
        last;
      }