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lib/Bio/RetrieveAssemblies.pm  view on Meta::CPAN

undef $VERSION;
package Bio::RetrieveAssemblies;
$Bio::RetrieveAssemblies::VERSION = '1.1.5';
use Moose;
use Bio::Perl; # force BioPerl to be picked up
use Getopt::Long qw(GetOptionsFromArray);
use Bio::RetrieveAssemblies::WGS;
use Bio::RetrieveAssemblies::AccessionFile;
with('Bio::RetrieveAssemblies::LoggingRole');

# ABSTRACT: Download assemblies from GenBank




has 'search_term'      => ( is => 'rw', isa => 'Str' );
has 'output_directory' => ( is => 'rw', isa => 'Str', default => 'downloaded_files' );
has 'file_type'        => ( is => 'rw', isa => 'Str', default => 'genbank' );
has 'organism_type'    => ( is => 'rw', isa => 'Str', default => 'BCT' );
has 'query'            => ( is => 'rw', isa => 'Str',      default  => '*' );
has 'annotation'       => ( is => 'rw', isa => 'Bool',     default  => 0 );
has 'args'             => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name'      => ( is => 'ro', isa => 'Str', required => 1 );

sub BUILD {
    my ($self) = @_;
    my ( $help, $file_type, $output_directory, $organism_type,$query,$annotation,$verbose,$cmd_version );
    GetOptionsFromArray(
        $self->args,
        'p|organism_type=s'    => \$organism_type,
        'f|file_type=s'        => \$file_type,
        'o|output_directory=s' => \$output_directory,
        'q|query=s'            => \$query,
        'a|annotation'         => \$annotation,
		'v|verbose'            => \$verbose,
		'version'              => \$cmd_version,
        'h|help'               => \$help,
    );
	
	if( $cmd_version)
	{
		print $self->_version();
		exit();
	}

    if ( $help || @{ $self->args } == 0 ) {
        print $self->usage_text();
        die;
    }

    $self->output_directory($output_directory) if ($output_directory);
    $self->file_type($file_type)               if ($file_type);
    $self->organism_type($organism_type)       if ($organism_type);
    $self->query($query)                       if ($query);
    $self->annotation($annotation)             if ($annotation);
	
    if ( defined($verbose) ) {
        $self->verbose($verbose);
        $self->logger->level(10000);
    }

    $self->search_term( $self->args->[0] );
}

sub _version
{
	my ($self) = @_;
	if(defined(Bio::RetrieveAssemblies->VERSION))
	{
	   return Bio::RetrieveAssemblies->VERSION ."\n";
    }
	else
	{
	   return "x.y.z\n";
	}
}


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

    return <<USAGE;