NAME

       Bio::Restriction::IO - Handler for sequence variation IO Formats

SYNOPSIS

           use Bio::Restriction::IO;

           $in  = Bio::Restriction::IO->new(-file => "inputfilename" ,
                                            -format => 'withrefm');
           my $res = $in->read; # a Bio::Restriction::EnzymeCollection

DESCRIPTION

       Bio::Restriction::IO is a handler module for the formats in the Restriction IO set, e.g.
       "Bio::Restriction::IO::xxx". It is the officially sanctioned way of getting at the format
       objects, which most people should use.

       The structure, conventions and most of the code is inherited from Bio::SeqIO. The main
       difference is that instead of using methods "next_seq", you drop "_seq" from the method
       name.

       Also, instead of dealing only with individual Bio::Restriction::Enzyme objects, "read()"
       will slurp in all enzymes into a Bio::Restriction::EnzymeCollection object.

       For more details, see documentation in Bio::SeqIO.

TO DO

       At the moment, these can be use mainly to get a custom set if enzymes in "withrefm" or
       "itype2" formats into Bio::Restriction::Enzyme or Bio::Restriction::EnzymeCollection
       objects.  Using "bairoch" format is highly experimental and is not recommmended at this
       time.

       This class inherits from Bio::SeqIO for convenience sake, though this should inherit from
       Bio::Root::Root.  Get rid of Bio::SeqIO inheritance by copying relevant methods in.

       "write()" methods are currently not implemented for any format except "base".  Using
       "write()" even with "base" format is not recommended as it does not support
       multicut/multisite enzyme output.

       Should additional formats be supported (such as XML)?

SEE ALSO

       Bio::SeqIO, Bio::Restriction::Enzyme, Bio::Restriction::EnzymeCollection

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

APPENDIX

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

   new
        Title   : new
        Usage   : $stream = Bio::Restriction::IO->new(-file => $filename,
                                                      -format => 'Format')
        Function: Returns a new seqstream
        Returns : A Bio::Restriction::IO::Handler initialised with
                  the appropriate format
        Args    : -file => $filename
                  -format => format
                  -fh => filehandle to attach to

   format
        Title   : format
        Usage   : $format = $stream->format()
        Function: Get the restriction format
        Returns : restriction format
        Args    : none

   read
        Title   : read
        Usage   : $renzs = $stream->read
        Function: reads all the restrction enzymes from the stream
        Returns : a Bio::Restriction::EnzymeCollection object
        Args    :

   write
        Title   : write
        Usage   : $stream->write($seq)
        Function: writes the $seq object into the stream
        Returns : 1 for success and 0 for error
        Args    : Bio::Restriction::EnzymeCollection object

   _guess_format
        Title   : _guess_format
        Usage   : $obj->_guess_format($filename)
        Function:
        Example :
        Returns : guessed format of filename (lower case)
        Args    :