Bio::Restriction::IO::base.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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)