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

    my $mono_mers =
        "|%{color:red}A%|"
      . $monomers->{A} . "|\n"
      . "|%{color:red}T%|"
      . $monomers->{T} . "|\n"
      . "|%{color:red}G%|"
      . $monomers->{G} . "|\n"
      . "|%{color:red}C%|"
      . $monomers->{C} . "|\n";

    my $gc_percentage =
      ( ( $monomers->{G} + $monomers->{C} ) /
          ( $monomers->{A} + $monomers->{T} + $monomers->{G} + $monomers->{C} )
      ) * 100;
    $gc_percentage = sprintf( "%.2f", $gc_percentage );

    my $REPORT = <<EOT;
h1. Bio::Tools::CodonOptTable

%{color:green}Report for $sequence_id%

%{color:red}Codon Adaptation Index (CAI) for sequence% : $cai

%{color:red}GC percentage for sequence% : $gc_percentage%

%{color:red}GENETIC CODE USED% : $genetic_code "--more about genetic code--":http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

%{background:#336699;color:white;padding:5px}++**CODON USAGE**++%

$codon_uses

%{background:#336699;color:white;padding:5px}++**Relative Synonimous Codon Usage (RSCU)**++%

$rscu_uses

result.html  view on Meta::CPAN

<h1>Bio::Tools::CodonOptTable</h1>

<p><span style="color:green" cite="http://">Report for gi|1255723|gb|U29581.1|ECU29581</span></p>

<p><span style="color:red" cite="http://">Codon Adaptation Index (CAI) for sequence</span> : 0.78</p>

<p><span style="color:red" cite="http://">GC percentage for sequence</span> : 50.82%</p>

<p><span style="color:red" cite="http://"><span class="caps">GENETIC CODE USED</span></span> : 1 <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi"><small>more about genetic code</small></a></p>

<p><span style="background:#336699;color:white;padding:5px" cite="http://"><big><b><span class="caps">CODON USAGE</span></b></big></span></p>

<table><tr><td><span style="color:red" cite="http://"><span class="caps">CODON</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span class="caps">GCC</span></span></td><td><span style="background:#f4f4f4" cite="http://"><span cl...


<p><span style="background:#336699;color:white;padding:5px" cite="http://"><big><b>Relative Synonimous Codon Usage (RSCU)</b></big></span></p>