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Bio/SeqFeature/Primer.pm  view on Meta::CPAN

=cut

sub new {
    my ($class, %args) = @_;

    # Legacy stuff
    my $sequence = delete $args{-sequence};
    if ($sequence) {
        Bio::Root::Root->deprecated(
            -message => 'Creating a Bio::SeqFeature::Primer with -sequence is deprecated. Use -seq instead.',
            -warn_version  => '1.006',
            -throw_version => '1.008',
        );
        $args{-seq} = $sequence;
    }

    # Initialize Primer object
    my $self = $class->SUPER::new(%args);
    my ($id) = $self->_rearrange([qw(ID)], %args);
    $id && $self->seq->id($id);
    $self->primary_tag('Primer');
    return $self;
}


# Bypass B::SF::Generic's location() when a string is passed (for compatibility)

sub location {
    my ($self, $location) = @_;
    if ($location) {
        if ( not ref $location ) {
            # Use location as a string for backward compatibility
            Bio::Root::Root->deprecated(
                -message => 'Passing a string to location() is deprecated. Pass a Bio::Location::Simple object or use start() and end() instead.',
                -warn_version  => '1.006',
                -throw_version => '1.008',
            );
            $self->{'_location'} = $location;
        } else {
            $self->SUPER::location($location);
        }
    }
    return $self->SUPER::location;
}


=head2 Tm()

 Title   : Tm()
 Usage   : my $tm = $primer->Tm(-salt => 0.05, -oligo => 0.0000001);
 Function: Calculate the Tm (melting temperature) of the primer
 Returns : A scalar containing the Tm.
 Args    : -salt  : set the Na+ concentration on which to base the calculation
                    (default=0.05 molar).
         : -oligo : set the oligo concentration on which to base the
                    calculation (default=0.00000025 molar).
 Notes   : Calculation of Tm as per Allawi et. al Biochemistry 1997
           36:10581-10594. Also see documentation at
           http://www.idtdna.com/Scitools/Scitools.aspx as they use this
           formula and have a couple nice help pages. These Tm values will be
           about are about 0.5-3 degrees off from those of the idtdna web tool.
           I don't know why.

           This was suggested by Barry Moore (thanks!). See the discussion on
           the bioperl-l with the subject "Bio::SeqFeature::Primer Calculating
           the PrimerTM"

=cut

sub Tm {
    my ($self, %args) = @_;
    my $salt_conc = 0.05; # salt concentration (molar units)
    my $oligo_conc = 0.00000025; # oligo concentration (molar units)
    if ($args{'-salt'}) {
        # Accept object defined salt concentration
        $salt_conc = $args{'-salt'};
    } 
    if ($args{'-oligo'}) {
        # Accept object defined oligo concentration
        $oligo_conc = $args{'-oligo'};
    }
    my $seqobj = $self->seq();
    my $length = $seqobj->length();
    my $sequence = uc $seqobj->seq();
    my @dinucleotides;
    my $enthalpy;
    my $entropy;
    # Break sequence string into an array of all possible dinucleotides
    while ($sequence =~ /(.)(?=(.))/g) {
        push @dinucleotides, $1.$2;
    }
    # Build a hash with the thermodynamic values
    my %thermo_values = ('AA' => {'enthalpy' => -7.9,
                                  'entropy'  => -22.2},
                         'AC' => {'enthalpy' => -8.4,
                                  'entropy'  => -22.4},
                         'AG' => {'enthalpy' => -7.8,
                                  'entropy'  => -21},
                         'AT' => {'enthalpy' => -7.2,
                                  'entropy'  => -20.4},
                         'CA' => {'enthalpy' => -8.5,
                                  'entropy'  => -22.7},
                         'CC' => {'enthalpy' => -8,
                                  'entropy'  => -19.9},
                         'CG' => {'enthalpy' => -10.6,
                                  'entropy'  => -27.2},
                         'CT' => {'enthalpy' => -7.8,
                                  'entropy'  => -21},
                         'GA' => {'enthalpy' => -8.2,
                                  'entropy'  => -22.2},
                         'GC' => {'enthalpy' => -9.8,
                                  'entropy'  => -24.4},
                         'GG' => {'enthalpy' => -8,
                                  'entropy'  => -19.9},
                         'GT' => {'enthalpy' => -8.4,
                                  'entropy'  => -22.4},
                         'TA' => {'enthalpy' => -7.2,
                                  'entropy'  => -21.3},
                         'TC' => {'enthalpy' => -8.2,
                                  'entropy'  => -22.2},