Bio::Restriction::IO::base(3)

NAME
Bio::Restriction::IO::base - base enzyme set

SYNOPSIS
Do not use this module directly. Use it via the Bio::Restriction::IO class.

DESCRIPTION
This class defines some base methods for restriction enzyme input and at the same time gives a base list of common enzymes.

FEEDBACK

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AUTHOR
Rob Edwards, redwards@utmem.edu

CONTRIBUTORS
Heikki Lehvaslaiho, heikki@ebi.ac.uk

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  read
 Title   : read
 Usage   : $renzs = $stream->read
 Function: reads all the restrction enzymes from the stream
 Returns : a Bio::Restriction::Restriction object
 Args    : none

  write
 Title   : write
 Usage   : $stream->write($renzs)
 Function: writes restriction enzymes into the stream
 Returns : 1 for success and 0 for error
 Args    : a Bio::Restriction::Enzyme
           or a Bio::Restriction::EnzymeCollection object

  Common REBASE parsing methods
The rest of the methods in this file are to be used by other REBASE parsers. They are not to be used outside subclasses of this base class. (They are 'protected' in the sense the word is used in Java.)

  _cuts_from_site
 Title   : _cuts_from_site
 Usage   : ($site, $cut, $comp_cut) = _cuts_from_site('ACGCGT(4/5)');
 Function: Separates cut positions from a single site string.
           Does nothing to site if it does not have the cut string
 Returns : array of site_string, forward_cut_position, reverse_cut_position
 Args    : recognition site string

  _meth
 Title   : _meth
 Usage   : ($pos, $meth) = $self->_meth('2(5)');
 Function: Separates methylation postion and coce from a string.
           Adjusts the postion depending on enzyme site length
           and symmetry
 Returns : array of position and methylation code
 Args    : 1. reference to Enzyme object
           2. methylation description string

  _coordinate_shift_to_cut
 Title   : _coordinate_shift_to_cut
 Usage   : $cut = $self->_coordinate_shift_to_cut($oricut, offset);
 Function: Adjust cut position coordinates to start from the
           first nucleotides of site
 Returns : Cut position in correct coordinates
 Args    : 1. Original cut position
           2. Length of the recognition site

  _make_multisites
 Title   : _make_multisites
 Usage   : $self->_make_multisites($collection, $first_enzyme, \@sites, \@mets)
 Function:

           Bless a Bio::Restriction::Enzyme (which is already part of
           the collection object) into
           Bio::Restriction::Enzyme::MultiSite and clone it as many
           times as there are alternative sites. The new objects are
           added into the collection and into others list of sister
           objects.

 Returns : nothing, does in place editing
 Args    : 1. a Bio::Restriction::EnzymeCollection
           2. a Bio::Restriction::Enzyme
           3. reference to an array of recognition site strings
           4. reference to an array of methylation code strings, optional

  _make_multicuts
 Title   : _make_multicuts
 Usage   : $self->_make_multicuts($collection, $first_enzyme, $precuts)
 Function:

           Bless a Bio::Restriction::Enzyme (which is already part of
           the collection object) into
           Bio::Restriction::Enzyme::MultiCut and clone it. The precut
           string is processed to replase the cut sites in the cloned
           object which is added into the collection. Both object
           refere to each other through others() method.

 Returns : nothing, does in place editing
 Args    : 1. a Bio::Restriction::EnzymeCollection
           2. a Bio::Restriction::Enzyme
           3. precut string, e.g. '12/7'

The examples we have of multiply cutting enzymes cut only four times. This protected method deals only with a string of two integers separated with a slash, e.g. '12/7'. The numbers represent the postions BEFORE the start of the recognition site, i.e. negative positions.

  _companies
 Title     : _companies
 Purpose   : Defines the companies that we know about
 Returns   : A hash
 Argument  : Nothing
 Comments  : An internal method to define the companies that we know about
             REBASE uses a code, and this converts the code to the real name
             (e.g. A = Amersham Pharmacia Biotech)