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

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to 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
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 Bugs
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://github.com/bioperl/bioperl-live/issues

AUTHOR
Rob Edwards, redwards@utmem.edu

CONTRIBUTORS
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Mark A. Jensen, maj-at-fortinbras-dot-us

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

  _xln_sub
 Title   : _xln_sub
 Function: Translates withrefm coords to Bio::Restriction coords
 Args    : Bio::Restriction::Enzyme object, scalar integer (cut posn)
 Note    : Used internally; pass as a coderef to the B:R::Enzyme
           constructor
 Note    : It is convenient for each format module to have its own
           version of this; not currently demanded by the interface.

  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

  verify_prototype
 Title     : verify_prototype
 Purpose   : checks enzyme against current prototype list (retrieved remotely)
 Returns   : returns TRUE if enzyme is prototype
 Argument  : Bio::Restriction::EnzymeI
 Comments  : This is an auxiliary method to retrieve and check an enzyme
             as a prototype.  It retrieves the current list, stores it
             as a singleton instance, then uses it to check the prototype
             and modify is_prototype() to true or false.  Use as follows:

             my $col = $io->read;
             for my $enz ($col->each_enzyme) {
                 print $enz->name.":".$enz->site."\n";
                 print "\t".$io->verify_prototype($enz)."\n";
             }

  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
 Note    : Not used in withrefm refactor/maj

  _meth
 Title   : _meth
 Usage   : ($pos, $meth) = $self->_meth('2(5)');
 Function: Separates methylation position and coce from a string.
           Adjusts the position 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
 Note    : Not used in withrefm.pm refactor/maj

  _make_multisites
 Title   : _make_multisites
 Usage   : $self->_make_multisites($first_enzyme, \@sites, \@mets)
 Function: Bless a Bio::Restriction::Enzyme  into
           Bio::Restriction::Enzyme::MultiSite and clone it as many
           times as there are alternative sites.
 Returns : nothing, does in place editing
 Args    : 1. a Bio::Restriction::Enzyme
           2. reference to an array of recognition site strings
           3. reference to an array of methylation code strings, optional

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

           Bless a Bio::Restriction::Enzyme into
           Bio::Restriction::Enzyme::MultiCut and clone it. The precut
           string is processed to replase the cut sites in the cloned
           object. Both objects refer to each other through others() method.

 Returns : nothing, does in place editing
 Args    : 1. a Bio::Restriction::Enzyme
           2. 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 positions 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)