/ 
BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Restriction::IO::base

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 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
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 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)