Bio::Restriction EnzymeCollection
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Restriction::EnzymeCollection - Set of restriction endonucleases
Package variables
No package variables defined.
Included modules
Bio::Restriction::Enzyme
Bio::Restriction::IO
Bio::Root::Root
Data::Dumper
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
newDescriptionCode
enzymesDescriptionCode
each_enzymeDescriptionCode
get_enzymeDescriptionCode
available_listDescriptionCode
longest_cutterDescriptionCode
blunt_enzymesDescriptionCode
cuttersDescriptionCode
Methods description
newcode    nextTop
 Title     : new
 Function  : Initializes the Restriction::EnzymeCollection object
 Returns   : The Restriction::EnzymeCollection object
 Arguments : optional named parameter -empty
Set parameter -empty to true if you do NOT want the collection be
populated by the default set of prototype type II enzymes.
Alternatively, pass an array of enzymes to -enzymes parameter.
enzymescodeprevnextTop
 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
each_enzymecodeprevnextTop
 Title     : each_enzyme
 Function  : get an array of enzymes
 Returns   : array of Bio::Restriction::Enzyme objects
 Arguments : -
get_enzymecodeprevnextTop
 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
available_listcodeprevnextTop
 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
longest_cuttercodeprevnextTop
 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
blunt_enzymescodeprevnextTop
  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  : 
This is an example of the kind of filtering better done by the scripts
using the rich collection of methods in Bio::Restriction::Enzyme.
cutterscodeprevnextTop
  Title     : cutters
  Function  : Gets a list of all the enzymes that recognize a
              certain size, e.g. 6-cutters
  Usage     : $cutters = $collection->cutters(6);
  Returns   : A reference to an array with all the enzyme names
              that are x cutters or 0 if none are defined
  Arguments : A positive number for the size of cutters to return
              OR
              A range: (-start => 6, -end => 8,
                        -inclusive => 1, -exclusive = 0 )
The default for a range is 'inclusive'
Methods code
newdescriptionprevnextTop
sub new {
    my($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 $in->read;
}
enzymesdescriptionprevnextTop
sub enzymes {
    my ($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;
}
each_enzymedescriptionprevnextTop
sub each_enzyme {
    my $self = shift;
    return @{$self->{'_all_enzymes'}};
}
get_enzymedescriptionprevnextTop
sub get_enzyme {
    my ($self, $name)=@_;
    return $self->{'_enzymes'}->{$name};
}
available_listdescriptionprevnextTop
sub available_list {
    my ($self, $size)=@_;
    return sort keys %{$self->{'_enzymes'}};
}
longest_cutterdescriptionprevnextTop
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;
}
blunt_enzymesdescriptionprevnextTop
sub blunt_enzymes {
    my $self=shift;
    my $bs = new Bio::Restriction::EnzymeCollection(-empty => 1);
    return $bs->enzymes(  grep { $_->overhang eq 'blunt' }  $self->each_enzyme );
}
cuttersdescriptionprevnextTop
sub cutters {
    my ($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
CUSTOM COLLECTIONSTop
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';
  }
COMMENTSTop
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)
SEE ALSOTop
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
FEEDBACKTop
Mailing Lists Top
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
Reporting BugsTop
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/
AUTHORTop
Rob Edwards, redwards@utmem.edu
CONTRIBUTORSTop
Heikki Lehvaslaiho, heikki@ebi.ac.uk
COPYRIGHTTop
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.
APPENDIXTop
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.
Manipulate the enzymes within the collectionTop
Filter enzymesTop