Summary

Bio::Restriction::EnzymeCollection - Set of restriction endonucleases

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

  use Bio::Restriction::EnzymeCollection;

  # create a set with a default enzymes
  my $collection = Bio::Restriction::EnzymeCollection;

  print "No of enzymes: ", scalar $collection->each_enzyme, "\n";

  # find something about a particular enzyme
  my $enz=$collection->get_enzyme('EcoRI');

  # and we know about some special types of enzymes.
  my $blunt_collection = $collection->blunt_enzymes; # enzymes without an overhang

  # see 'CUSTOM COLLECTIONS' below  for more options

  # the most common selection criteria is how many times the enzymes
  # cuts. This can be estimated using the length and specificity of
  # the recognition site

  # enzymes that have euivalent of  6bp recognition sequence
  my $six_cutters=$collection->cutters(6);

  # all rare cutters
  my $rare_cutters=$collection->cutters(-start=>6, -end=>8);

Description

Bio::Restriction::EnzymeCollection represents a collection of
restriction enzymes.
If you create a new collection directly rather than from a REBASE
format file using Bio::RestrictionIO, it will be populated by a
default set of protype, typeII enzymes with site and cut information
only.
Use Bio::Restriction::Analysis to figure out which enzymes are
available and where they cut your sequence.

Methods

Methods description

 Title     : new
 Function  : Initializes the Restriction::EnzymeCollection object
 Returns   : The Restriction::EnzymeCollection object
 Arguments : optional named parameter -empty

 Title     : enzyme
 Function  : add/get method for enzymes and enzyme collections
 Returns   : object itself
 Arguments : array of Bio::Restriction::Enzyme and
             Bio::Restriction::EnzymeCollection objects

 Title     : each_enzyme
 Function  : get an array of enzymes
 Returns   : array of Bio::Restriction::Enzyme objects
 Arguments : -

 Title     : get_enzyme
 Function  : Gets a Bio::Restriction::Enzyme object for the enzyme name
 Returns   : A Bio::Restriction::Enzyme object or undef
 Arguments : An enzyme name that is in the collection

 Title     : available_list
 Function  : Gets a list of all the enzymes that we know about
 Returns   : A reference to an array with all the enzyme names
             that we have defined or 0 if none are defined
 Arguments : Nothing
 Comments  : Note, I maintain this for backwards compatibility,
             but I don't like the name as it is very ambiguous

 Title     : longest_cutter
 Function  : Gets the enzyme with the longest recognition site
 Returns   : A Bio::Restriction::Enzyme object
 Arguments : Nothing
 Comments  : Note, this is used by Bio::Restriction::Analysis
             to figure out what to do with circular sequences

  Title     : blunt_enzymes
  Function  : Gets a list of all the enzymes that are blunt cutters
  Returns   : A reference to an array with all the enzyme names that
              are blunt cutters or 0 if none are defined
  Arguments : Nothing
  Comments  : 

  Title     : cutters
  Function  : Gets a list of all the enzymes that recognize a
              certain size, e.g. 6-cutters
  Usage     : $cutters = $collection->cutters(6);
  Returns   : A reference to an array with all the enzyme names
              that are x cutters or 0 if none are defined
  Arguments : A positive number for the size of cutters to return
              OR
              A range: (-start => 6, -end => 8,
                        -inclusive => 1, -exclusive = 0 )

Methods code

sub new {

    my($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    my ($empty) =
            $self->_rearrange([qw(
                                  EMPTY
                                 )], @args);

    $self->{'_all_enzymes'} = [];
    $self->{'_enzymes'} = {};

    return $self if $empty;

    # the default set of enzymes
    my $in  = Bio::Restriction::IO->new(-verbose => $self->verbose);
    return $in->read;

}

sub enzymes {

    my ($self, @enzs)=@_;
    foreach my $e (@enzs) {
        if ( ref $e eq '') {
            print "|$e|\n";
        }
        elsif ($e->isa('Bio::Restriction::EnzymeI')) {
            push(@{$self->{'_all_enzymes'}},$e);
            $self->{'_enzymes'}->{$e->name} = $e;
        }
        elsif ($e->isa('Bio::Restriction::EnzymeCollection')) {
           $self->enzymes($e->each_enzyme);
        } else {
            my $r = 1;
            $self->warn("EnzymeCollection can not deal with ".
                        ref($e)." objects");
        }
    }
    return $self;

}

sub each_enzyme {

    my $self = shift;
    return @{$self->{'_all_enzymes'}};

}

sub get_enzyme {

    my ($self, $name)=@_;
    return $self->{'_enzymes'}->{$name};

}

sub available_list {

    my ($self, $size)=@_;
    return sort keys %{$self->{'_enzymes'}};

}

sub longest_cutter {

    my ($self)=@_;
    my $longest=0; my $longest_enz='.';
    foreach my $enz ($self->each_enzyme) {
     my $len=$enz->recognition_length;
     if ($len > $longest) {$longest=$len; $longest_enz=$enz}
    }
    return $longest_enz;

}

sub blunt_enzymes {

    my $self=shift;
    my $bs = new Bio::Restriction::EnzymeCollection(-empty => 1);
    return $bs->enzymes(  grep { $_->overhang eq 'blunt' }  $self->each_enzyme );

}

sub cutters {

    my ($self) = shift;

    return unless @_; # no argument

    if (scalar @_ == 1 ) {
        my $size = shift;
        $self->throw("Need a positive number [$size]")
            unless $size =~ /[+]?[\d\.]+/;

        my $bs = new Bio::Restriction::EnzymeCollection(-empty => 1);

        foreach my $e ($self->each_enzyme) {
            ##print $e->name, ": ", $e->cutter, "\n"  if $e->cutter == $size;
            $bs->enzymes($e) if $e->cutter == $size;
        }
        return $bs;
        #return $bs->enzymes(  grep { ($_->cutter == $size) }  $self->each_enzyme );

    } else { # named arguments

        my ($start, $end, $inclusive, $exclusive ) =
            $self->_rearrange([qw(
                                  START
                                  END
                                  INCLUSIVE
                                  EXCLUSIVE
                                 )], @_);

        $self->throw("Start needs a positive number [$start]")
            unless $start =~ /[+]?[\d\.]+/;
        $self->throw("End needs a positive number [$end]")
            unless $end =~ /[+]?[\d\.]+/;

        my $limits;
        $inclusive = 1 if $inclusive or not $exclusive;
        $inclusive = 0 if $exclusive;

        my $bs = new Bio::Restriction::EnzymeCollection(-empty => 1);
        if ($inclusive) {
            foreach my $e ($self->each_enzyme) {
                $bs->enzymes($e) if $e->cutter >= $start and $e->cutter <= $end;
            }
        } else {
            foreach my $e ($self->each_enzyme) {
                $bs->enzymes($e) if $e->cutter > $start and $e->cutter < $end;
            }
        }
        return $bs;
    }

}

General documentation

Note, that the underlying Enzyme objects are much more rich and allow
more complicated selections than the predefinend methods. The way to
create a custom subset is as follows:

  my $initial_collection;
  my $new_collection = Bio::Restriction::EnzymeCollection(-empty => 1);
  foreach $enzyme ($initial_collection) {
      # this selects only type II enzymes
      $new_collection($enzyme) if $enzyme->type eq 'II';
  }

I am trying to make this backwards compatible with
Bio::Tools::RestrictionEnzyme. Undoubtedly some things will break, but
we can fix things as we progress.....!
I have added another comments section at the end of this POD that
discusses a couple of areas I know are broken (at the moment)

Bio::Restriction::IO - read in enzymes from REBASE files
(s
Bio::Restriction::Analysis - figure out what enzymes cut a sequence
(start here)
Bio::Restriction::Enzyme - defining a single restriction enzyme

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

    bioperl-l@bioperl.org             - General discussion
    http://bioperl.org/MailList.shtml - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:

     bioperl-bugs@bio.perl.org
     http://bugzilla.bioperl.org/

Rob Edwards, redwards@utmem.edu

Heikki Lehvaslaiho, heikki@ebi.ac.uk

Copyright (c) 2003 Rob Edwards.
Some of this work is Copyright (c) 1997-2002 Steve A. Chervitz. All
Rights Reserved.
This module is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.

Methods beginning with a leading underscore are considered private and
are intended for internal use by this module. They are not considered
part of the public interface and are described here for documentation
purposes only.