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lib/Bio/MUST/Apps/TwoScalp/Seq2Seq.pm  view on Meta::CPAN

    my $query_seqs = $self->query_seqs;
    my $parser = $blastdb->blast($query_seqs, $args);
    #### [S2S] XML BLASTP/N: $parser->filename

    my $bo = $parser->blast_output;
    return unless $bo;

    my $sort_method = $self->single_hsp ? 'score' : 'hit_start';

    QUERY:
    for my $query ( $bo->all_iterations ) {

        my $query_id = $query_seqs->long_id_for( $query->query_def );
        ##### [S2S] Aligning: $query_id

        my @templates;
        my @template_seqs;
        my $best_coverage = 0;

        TEMPLATE:
        for my $template ( $query->all_hits ) {