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

package Bio::RetrieveAssemblies::AccessionFile;
$Bio::RetrieveAssemblies::AccessionFile::VERSION = '1.1.5';
use Moose;
use Bio::RetrieveAssemblies::Exceptions;
use File::Path qw(make_path);
use File::Basename;
use File::Copy;
use Data::Validate::URI qw(is_uri);
use Bio::SeqIO;    # force dependancy on Bio::Perl so that you get bp_genbank2gff3.pl
use Moose::Util::TypeConstraints;
with('Bio::RetrieveAssemblies::LoggingRole');

# ABSTRACT: For a given accession get the file of annotation or sequence


enum 'FileType', [qw(genbank fasta gff)];

has 'accession'        => ( is => 'ro', isa => 'Str',      required => 1 );
has 'output_directory' => ( is => 'ro', isa => 'Str',      default  => 'downloaded_files' );
has 'file_type'        => ( is => 'rw', isa => 'FileType', default  => 'genbank' );
has '_base_url'        => ( is => 'ro', isa => 'Str',      default  => 'http://www.ncbi.nlm.nih.gov/Traces/wgs/?download=' );
has '_converter_exec'  => ( is => 'ro', isa => 'Str',      default  => 'bp_genbank2gff3.pl' );
has 'url_to_file'      => ( is => 'ro', isa => 'ArrayRef', lazy     => 1, builder => '_build_url_to_file' );
has 'output_filename'  => ( is => 'ro', isa => 'Str',      lazy     => 1, builder => '_build_output_filename' );

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

    my @url_to_file;
    if ( $self->file_type eq 'fasta' ) {
        push( @url_to_file, $self->_base_url . $self->accession . '.1.fsa_nt.gz' );
        push( @url_to_file, $self->output_directory . '/' . $self->accession . '.1.fsa_nt.gz' );
    }
    else {
        push( @url_to_file, $self->_base_url . $self->accession . '.1.gbff.gz' );
        push( @url_to_file, $self->output_directory . '/' . $self->accession . '.1.gbff.gz' );
    }
    return \@url_to_file;
}

sub _build_output_filename {
    my ($self) = @_;
    my $output_filename = $self->url_to_file->[1];
    if ( $self->file_type eq "gff" ) {
        $output_filename .= '.gff';
    }
    return $output_filename;
}

sub download_file {
    my ($self) = @_;
    make_path( $self->output_directory );

    if ( is_uri( $self->url_to_file->[0] ) ) {
		my $quiet_str = "-q";
		if($self->verbose)
		{
			$quiet_str = "";
		}
		
		my $cmd = "wget $quiet_str -O ".$self->url_to_file->[1]." '".$self->url_to_file->[0] ."'";
		$self->logger->info("Downloading accession: ".$self->accession);
		$self->logger->info("Download cmd: ".$cmd);
		system($cmd ) ;
		#or Bio::RetrieveAssemblies::Exceptions::CouldntDownload->throw( error => "Unable to get remote page ".$self->url_to_file->[0] )
    }
    else {
        copy( $self->url_to_file->[0], $self->url_to_file->[1] )
          or Bio::RetrieveAssemblies::Exceptions::FileCopyFailed->throw( error => "Copy failed: $!" );
    }

    if ( $self->file_type eq "gff" ) {
        $self->_convert_gb_to_gff();
    }
    return 1;
}

sub _convert_gb_to_gff_cmd {
    my ($self) = @_;
	my $quiet_str =  "--quiet";
	if($self->verbose)
	{
		$quiet_str = "";