Bio::Restriction EnzymeCollection
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Summary
Bio::Restriction::EnzymeCollection - Set of restriction endonucleases
Package variables
No package variables defined.
Included modules
Bio::Restriction::Enzyme
Bio::Restriction::IO
Data::Dumper
Inherit
Bio::Root::Root
Synopsis
  use Bio::Restriction::EnzymeCollection;
# Create a collection with the default enzymes. my $default_collection = Bio::Restriction::EnzymeCollection->new(); # Or create a collection from a REBASE 'withrefm' file obtained from # ftp://ftp.neb.com/pub/rebase/. (See Bio::Restriction::IO for more
# information.)
my $rebase = Bio::Restriction::IO->new(
-file => 'withrefm.610',
-format => 'withrefm' );
my $rebase_collection = $rebase->read();
# Or create an empty collection and set the enzymes later. See # 'CUSTOM COLLECTIONS' below for more information. my $empty_collection = Bio::Restriction::EnzymeCollection->new( -empty => 1 ); # Get an array of Bio::Restriction::Enzyme objects from the collection. my @enzymes = $default_collection->each_enzyme(); # Get a Bio::Restriction::Enzyme object for a particular enzyme by name. my $enz = $default_collection->get_enzyme( 'EcoRI' ); # Get a Bio::Restriction::EnzymeCollection object containing the enzymes # that have the equivalent of 6-bp recognition sequences. my $six_cutters = $default_collection->cutters( 6 ); # Get a Bio::Restriction::EnzymeCollection object containing the enzymes # that are rare cutters. my $rare_cutters = $default_collection->cutters( -start => 6, -end => 8 ); # Get a Bio::Restriction::EnzymeCollection object that contains enzymes # that generate blunt ends: my $blunt_cutters = $default_collection->blunt_enzymes(); # See 'CUSTOM COLLECTIONS' below for an example of creating a # Bio::Restriction::EnzymeCollection object with a specified subset of # enzymes using methods provided by the Bio::RestrictionEnzyme class.
Description
Bio::Restriction::EnzymeCollection represents a collection of
restriction enzymes.
If you create a new collection directly rather than from a REBASE
file using Bio::Restriction::IO, it will be populated by a
default set of 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, $enzymes) =
            $self->_rearrange([qw(
                                  EMPTY
                                  ENZYMES
                                 )], @args);

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

    return $self if $empty;


    if ($enzymes) {
	# as advertised in pod/maj
$self->throw( "Arg to -enzymes must be an arrayref to Bio::Restriction::Enzyme objects") unless ref($enzymes) eq 'ARRAY'; $self->enzymes(@$enzymes); return $self; } else { # 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;
}

#
# method to remove duplicates?
#
}
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, $size)=@_;
    my @keys = sort keys %{$self->{'_enzymes'}};
    return @keys;
}
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 = Bio::Restriction::EnzymeCollection->new(-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; my @sizes; (ref $size eq 'ARRAY') ? push @sizes, @{$size} : push @sizes, $size; my $bs = Bio::Restriction::EnzymeCollection->new(-empty => 1); for my $size (@sizes) { $self->throw("Need a positive number [$size]") unless $size =~ /[+]?[\d\.]+/; foreach my $e ($self->each_enzyme) { ##print $e->name, ": ", $e->cutter, "\n" if $e->cutter == $size;
$bs->enzymes($e) if $e->cutter == $size; } } return $bs; } else { # named arguments
my ($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 $bs = Bio::Restriction::EnzymeCollection->new(-empty => 1); if ($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; } } 1;
}
General documentation
CUSTOM COLLECTIONSTop
Note that the underlying Bio::Restriction::Enzyme objects have a rich
variety of methods that allow more complicated selections than the methods
that are defined by Bio::Restriction::EnzymeCollection.
For example, the way to create a custom collection of Type II enzymes
is as follows:
  my $complete_collection =
Bio::Restriction::EnzymeCollection->new();
my $type_ii_collection =
Bio::Restriction::EnzymeCollection->new( -empty => 1 );
$type_ii_collection->enzymes(
grep { $_->type() eq 'II' } $complete_collection->each_enzyme() );
SEE ALSOTop
Bio::Restriction::IO - read in enzymes from REBASE files
Bio::Restriction::Analysis - figure out what enzymes cut a sequence
Bio::Restriction::Enzyme - define 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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Rob Edwards, redwards@utmem.edu
CONTRIBUTORSTop
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
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