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

            'frequency' => $codons->{$single_codon},
            'aa_name'   => $aa_name,
        };
    }
    $self->{'codons'} = $myCodons;

    return 1;
}

#    Function : Calculate the RSCU(Relative Synonymous Codons Uses).
#    Note     : The formula is used in the following references.
#	 http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=3547335

sub _calculate_rscu {
    my $self = shift;

    my $codons = $self->{'codons'};

    my ( $rscu, @myCodons, %rscu_max_table );

    foreach my $each_codon ( keys %$codons ) {

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

            aa_name       => $amino,
            rscu          => $rscu,
            total_aa_comb => $count,
            all_fre_aa    => $all_freq_aa,
          };
    }
    return ( \@myCodons, \%rscu_max_table );
}

#    Function : Calculate the RAC (Relative Adaptiveness of a Codon).
#    Note     : The formula is used in the following references.
#	 http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=3547335

sub _calculate_rac {
    my ( $self, $codons, $max_rscu ) = @_;
    my ( $rac, @myCodons );

    foreach my $each_codon (@$codons) {
        my $amino = $each_codon->{'aa_name'};
        my $rscu  = $each_codon->{'rscu'};
        if ($amino) {