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

	$self->logger->info("Downloading list of bad assembly accession numbers from RefWeak");
    return Bio::RetrieveAssemblies::RefWeak->new(logger => $self->logger, verbose => $self->verbose)->accessions();
}

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

    if ( $self->annotation ) {
        # Only get files with annotation
        return "http://www.ncbi.nlm.nih.gov/Traces/wgs/?page=1&term=" . $self->query
          . "&order=prefix&dir=a&state=live&project=WGS&update_date=any&create_date=any&have_annot_contigs=on&have_annot_scaffolds=on&retmode=text&size=all";
    }
    else {
        # Get everything bar TSA
        return "http://www.ncbi.nlm.nih.gov/Traces/wgs/?&size=100&term=" . $self->query
          . "&project=WGS&order=prefix&dir=asc&version=last&state=live&update_date=any&create_date=any&retmode=text&size=all";
    }
}

sub _filter_out_line {
    my ( $self, $columns ) = @_;