File Coverage

blib/lib/Bio/GeneDesign/RestrictionEnzymes.pm

Criterion	Covered	Total	%
statement	65	65	100.0
branch	8	10	80.0
condition			n/a
subroutine	10	10	100.0
pod			n/a
total	83	85	97.6

#
# GeneDesign module for sequence segmentation
#

=head1 NAME

Bio::GeneDesign::RestrictionEnzymes

=head1 VERSION

Version 5.56

=head1 DESCRIPTION

GeneDesign functions for handling restriction enzymes

=head1 AUTHOR

Sarah Richardson

=cut

package Bio::GeneDesign::RestrictionEnzymes;

use Exporter;
use Bio::GeneDesign::Basic qw(:GD);
use Bio::GeneDesign::RestrictionEnzyme;
use Carp;

use strict;
use warnings;

our $VERSION = 5.56;

use base qw(Exporter);
our @EXPORT_OK = qw(
  _define_sites
  _define_site_status
  _parse_enzyme_list
  $VERSION
);
our %EXPORT_TAGS =  (GD => \@EXPORT_OK);

=head2 define_sites()

Generates a hash reference where the keys are enzyme names and the values are
L objects.

=cut

sub _define_sites
{
  my ($file) = @_;
  open (my $REFILE, '<', $file) || croak ("Can't find $file!\n");
  my $ref = do { local $/ = <$REFILE> };
  close $REFILE;
  my @data = split(m{\n}x, $ref);
  my %RES;
  my @lines = grep {$_ !~ m{^ \# }x} @data;
  foreach my $line (@lines)
  {
    my ($name, $site, $temp, $inact, $buf1, $buf2, $buf3, $buf4, $bufu, $dam,
        $dcm, $cpg, $score, $star, $vendor, $aggress) = split("\t", $line);
    my $buffhsh = {NEB1 => $buf1, NEB2 => $buf2, NEB3 => $buf3,
                   NEB4 => $buf4, Other => $bufu};
    $star = undef unless ($star eq 'y');
    my $re = Bio::GeneDesign::RestrictionEnzyme->new(
      -id => $name,
      -cutseq => $site,
      -temp   => $temp,
      -tempin => $inact,
      -score  => $score,
      -methdam => $dam,
      -methdcm => $dcm,
      -methcpg => $cpg,
      -staract => $star,
      -vendors => $vendor,
      -buffers => $buffhsh,
      -aggress => $aggress
    );
    $RES{$re->{id}} = $re;
  }
  #Make exclusion lists
  foreach my $re (values %RES)
  {
    my $rid = $re->{id};
    my %excl;
    foreach my $ar (sort grep {$_->{id} ne $rid} values %RES)
    {
      foreach my $arreg (@{$ar->{regex}})
      {
        $excl{$ar->{id}}++ if ($re->{recseq} =~ $arreg)
      }
      foreach my $rereg (@{$re->{regex}})
      {
        $excl{$ar->{id}}++ if ($ar->{recseq} =~ $rereg)
      }
    }
    my @skips = sort keys %excl;
    $re->exclude(\@skips);
  }
  return \%RES;
}

=head2 define_site_status

Generates a hash describing the restriction count of a nucleotide sequence.

  Arguments: nucleotide sequence as a string
             an arrayref of L objects

  Returns: reference to a hash where the keys are enzyme ids and the value is
            a count of their occurence in the nucleotide sequence

=cut

sub _define_site_status
{
  my ($seq, $RES) = @_;
  my $SITE_STATUS = {};
  foreach my $re (@{$RES})
  {
    my $tmphsh = $re->positions($seq);
    $SITE_STATUS->{$re->id} = scalar keys %{$tmphsh};
  }
  return $SITE_STATUS;
}

=head2 _parse_enzyme_list

=cut

sub _parse_enzyme_list
{
  my ($path) = @_;
  open (my $REFILE, '<', $path) || croak ("Can't read $path!\n");
  my $ref = do { local $/ = <$REFILE> };
  close $REFILE;
  my @list = split m{\s}x, $ref;
  return \@list;
}

1;

__END__