mono and dinucleotide frequency methods for Bio::SeqUtils

gistfile1.txt

=head2 monofreq

 Title   : monofreq
 Usage   : $seq = Bio::SeqUtils->monofreq($seq)
 Function: Method for determining the mononucleotide frequencies of
           a DNA sequence

 Returns : Array of mononucleotide frequencies T, C, G, A
 Args    : none

=cut

sub monofreq {
   my ($self, $seq) = @_;

   $seq->isa('Bio::PrimarySeqI') ||
           $self->throw("Not a Bio::PrimarySeqI object but [$self]");
   $seq->alphabet =~ /DNA/i ||
           $self->throw('Not a DNA sequence');

   my $DNA = $seq->seq;
   my $Total = $seq->length;
   my $T=($DNA=~tr/T//);   my $C=($DNA=~tr/C//);   my $G=($DNA=~tr/G//);   my $A=($DNA=~tr/A//);
   my $Tper = $T/$Total;   my $Cper = $C/$Total;   my $Gper = $G/$Total;   my $Aper = $A/$Total;

   return ($Tper, $Cper, $Gper, $Aper);
}

=head2 dinucbias

 Title   : dinucbias
 Usage   : $seq = Bio::SeqUtils->dinucbias($seq)
 Function: Method for determining the dinucleotide bias
           frequencies for a DNA sequence

 Returns : Array of dinucleotide bias frequencies TT, TC, ...CT,..GT,..AT,AC,AG,AA
 Args    : none

=cut

sub dinucbias {
   my ($self, $seq) = @_;

   $seq->isa('Bio::PrimarySeqI') ||
           $self->throw("Not a Bio::PrimarySeqI object but [$self]");
   $seq->alphabet =~ /DNA/i ||
           $self->throw('Not a DNA sequence');

   # needs implemented
}