File Coverage

blib/lib/Bio/GeneDesign/Oligo.pm

Criterion	Covered	Total	%
statement	12	39	30.7
branch	0	10	0.0
condition	0	2	0.0
subroutine	4	7	57.1
pod			n/a
total	16	58	27.5

#
# GeneDesign module for sequence segmentation
#

=head1 NAME

Bio::GeneDesign::Oligo

=head1 VERSION

Version 5.56

=head1 DESCRIPTION


=head1 AUTHOR

Sarah Richardson .

=cut

package Bio::GeneDesign::Oligo;
require Exporter;

use Bio::GeneDesign::Basic qw(:GD);
use strict;
use warnings;

our $VERSION = 5.56;

use base qw(Exporter);
our @EXPORT_OK = qw(
  _make_amplification_primers
  _filter_homopolymer
  _check_for_homopolymer
  $VERSION
);
our %EXPORT_TAGS =  (GD => \@EXPORT_OK);

=head1 Functions

=head2 _filter_homopolymer()

=cut

sub _filter_homopolymer
{
  my ($seqarr, $length) = @_;
  my @newarr = ();
  foreach my $seq (@{$seqarr})
  {
    push @newarr, $seq if (! _check_for_homopolymer($seq, $length));
  }
  return \@newarr;
}

=head2 _check_for_homopolymer()

=cut

sub _check_for_homopolymer
{
  my ($seq, $length) = @_;
  $length = $length || 5;
  return 1 if ($length <= 1);
  return 1 if $seq =~ m{A{$length}|T{$length}|C{$length}|G{$length}}msxi;
  return 0;
}

=head2 _make_amplification_primers()

=cut

sub _make_amplification_primers
{
  my ($sequence, $temperature) = @_;

  my $left_length = 5;
  my $lprimer = substr($sequence, 0, $left_length);
  while (_melt($lprimer) < $temperature)
  {
    $left_length++;
    last if ($left_length > 45);
    $lprimer = substr($sequence, 0, $left_length)
  }

  my $right_end = length($sequence);
  my $right_length = 5;
  my $rprimer = substr($sequence, $right_end - $right_length, $right_length);
  while (_melt($rprimer) < $temperature)
  {
    $right_length++;
    last if ($right_length > 45);
    $rprimer = substr($sequence, $right_end - $right_length, $right_length);
  }
  $rprimer = _complement($rprimer, 1);

  return ($lprimer, $rprimer);
}

1;

__END__