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Bio::Restriction::IO(3User Contributed Perl DocumentatiBio::Restriction::IO(3)

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	:

perl v5.24.1			  2017-07-08	       Bio::Restriction::IO(3)

NAME | SYNOPSIS | DESCRIPTION | TO DO | SEE ALSO | FEEDBACK | AUTHOR | CONTRIBUTORS | APPENDIX

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