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lib/Bio/Tools/CodonOptTable.pm  view on Meta::CPAN

}

sub prefered_codon {
    my ( $self, $codons ) = @_;
    my $prefered_codon;
    for my $each_aa (@$codons) {
        my $aa_name   = $each_aa->{'aa_name'};
        my $rscu      = $each_aa->{'rscu'};
        my $codon     = $each_aa->{'codon'};
        my $frequency = $each_aa->{'frequency'};

        if ( !defined( $prefered_codon->{$aa_name} )
            || ( $prefered_codon->{$aa_name} < $rscu ) )
        {
            $prefered_codon->{$aa_name} = $codon;
        }
    }
    return $prefered_codon;
}

sub generate_graph {
    my ( $self, $codons, $output_file ) = @_;

    my ( @x_axis_labels, @rscu, @rac, @x_axis_values, @codons_table,
        @codon_freq );
    my $y_axis_max       = 8;
    my @category_colours = qw(red dgreen);
    my $bar_graph        = new GD::Graph::bars( 1000, 500 );

    foreach my $each_aa (@$codons) {
        if ( $each_aa->{'aa_name'} ) {
            push( @codons_table,
                $each_aa->{'aa_name'} . "(" . $each_aa->{'codon'} . ")" );
            push( @codon_freq, $each_aa->{'frequency'} );
            push( @x_axis_labels,
                    $each_aa->{'codon'} . "("
                  . $each_aa->{'frequency'} . ")" . "-"
                  . $each_aa->{'aa_name'} );
            push( @rscu, $each_aa->{'rscu'} );
            push( @rac,  $each_aa->{'rac'} );
        }
    }

    my @bar_graph_table;
    push( @bar_graph_table, \@x_axis_labels );
    push( @bar_graph_table, \@rscu );
    push( @bar_graph_table, \@rac );

    $bar_graph->set(
        title =>
'Graph Representing : Relative Synonymous Codons Uses and Relative Adaptiveness of a Codon for '
          . $self->display_id,
        y_label     => 'RSCU and RAC values',    #y-axis label
        y_max_value => $y_axis_max,              #the max value of the y-axis
        y_min_value => 0
        , #the min value of y-axis, note set below 0 if negative values are required
        y_tick_number    => 20,      #y-axis scale increment
        y_label_skip     => 1,       #label every other y-axis marker
        box_axis         => 0,       #do not draw border around graph
        line_width       => 2,       #width of lines
        legend_spacing   => 5,       #spacing between legend elements
        legend_placement => 'RC',    #put legend to the centre right of chart
        dclrs => \@category_colours
        ,    #reference to array of category colours for each line
        bgclr             => 'red',
        long_ticks        => 0,
        tick_length       => 3,
        x_labels_vertical => 1,
    ) || die "\nFailed to create line graph: $bar_graph->error()";

    $bar_graph->set_legend( 'RSCU Value', 'RAC Value' );

    my $plot = $bar_graph->plot( \@bar_graph_table );

    my $line_file = $output_file;
    open( GPH, ">$line_file" )
      || die("\nFailed to save graph to file: $line_file. $!");
    binmode(GPH);
    print GPH $plot->gif();
    close(GPH);
}

sub generate_report {
    my ( $self, $out_file ) = @_;

    my $myCodons     = $self->rscu_rac_table();
    my $sequence_id  = $self->id;
    my $genetic_code = $self->{genetic_code};
    my $monomers     = $self->{monomers_count};
    my $cai          = $self->calculate_cai($myCodons);

    my %colors = (
        'Ala'  => '#f4f4f4', 'Arg'  => '#FF99FF', 'Asn'  => '#CC99CC',
        'Asp'  => '#99FFCC', 'Cys'  => '#99CC99', 'Gln'  => '#CCFF00',
        'Glu'  => '#FF00CC', 'Gly'  => '#33FFCC', 'His'  => '#66CCFF',
        'Ile'  => '#c9c9c9', 'Leu'  => '#CCFFFF', 'Lys'  => '#FFFFCC',
        'Met'  => '#FFFF66', 'Phe'  => '#FFCC00', 'Pro'  => '#F4F4F4',
        'Ser'  => '#FF99FF', 'Thr'  => '#CC99CC', 'Trp'  => '#99FFCC',
        'Tyr'  => '#CCFF00', 'Val'  => '#33FFCC', 'Asx'  => '#6666CC',
        'glx'  => '#FF00CC', 'Xaa'  => '#cccccc', 'Stop' => '#f8f8f8'
    );

    my $codons  = "|%{color:red}CODON%|";
    my $aa_name = "|%{color:red}AMINOACID%|";
    my $counts  = "|%{color:red}COUNT%|";
    my $rscu    = "|%{color:red}RSCU%|";
    my $rac     = "|%{color:red}RAC%|";

    foreach my $each_codon (@$myCodons) {
        my $frequency  = $each_codon->{frequency} || 'O';
        my $amino_acid = $each_codon->{aa_name};
        my $codon      = $each_codon->{codon};
        my $rscu_value = $each_codon->{rscu};
        my $rac_value  = $each_codon->{rac};
        my $aa_color   = $colors{$amino_acid};

        $codons  .= "%{background:$aa_color}$codon%|";
        $aa_name .= "%{background:$aa_color}$amino_acid%|";
        $counts  .= "%{background:$aa_color}$frequency%|";
        $rscu    .= "%{background:$aa_color}$rscu_value%|";
        $rac     .= "%{background:$aa_color}$rac_value%|";
    }
    my $codon_uses = "$codons\n$aa_name\n$counts\n";
    my $rscu_uses  = "$codons\n$aa_name\n$rscu\n";
    my $rac_uses   = "$codons\n$aa_name\n$rac\n";
    my $mono_mers =
        "|%{color:red}A%|"
      . $monomers->{A} . "|\n"
      . "|%{color:red}T%|"
      . $monomers->{T} . "|\n"
      . "|%{color:red}G%|"