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lib/Bio/Tradis/CombinePlots.pm  view on Meta::CPAN

sub _write_stats {
    my ( $self, $id, $seq_len ) = @_;
    my $combined_dir = $self->combined_dir;
    my $comb_plot = "$combined_dir/$id.insert_site_plot";

    #my $seq_len = `wc $comb_plot | awk '{print \$1}'`;
    #chomp($seq_len);
    my $uis = `grep -c -v "0 0" $comb_plot`;
    chomp($uis);
    my $sl_per_uis = "NaN";
    $sl_per_uis = $seq_len / $uis if($uis > 0);

    my $stats = "$id,$seq_len,$uis,$sl_per_uis\n";
    print { $self->_stats_handle } $stats;

    return 1;
}

sub _abs_path_list {
    my ( $self, $files ) = @_;

lib/Bio/Tradis/RunTradis.pm  view on Meta::CPAN

        my $plotname = $self->_plotname($si);
        system(
"gunzip -c $temporary_directory/$plotname > $temporary_directory/tmp.plot"
        );
        my $uis = `grep -c -v "0 0" $temporary_directory/tmp.plot`;
        chomp($uis);
        $total_uis += $uis;
        $stats .= "$uis,";
        my $seqlen = ${$seq_info}{$si};
        $total_seq_len += $seqlen;
        my $uis_per_seqlen = "NaN";
        $uis_per_seqlen = $seqlen / $uis if ( $uis > 0 );
        chomp($uis_per_seqlen);
        $stats .= "$uis_per_seqlen,";
    }
    $stats .= "$total_uis,";
    my $t_uis_p_l = "NaN";
    $t_uis_p_l = $total_seq_len / $total_uis if ( $total_uis > 0 );
    $stats .= "$t_uis_p_l\n";
    print { $self->_stats_handle } $stats;
}

sub _write_stats_header {
    my ($self)   = @_;
    my @seqnames = keys %{ $self->_sequence_info };
    my @fields   = (
        "File",