Bio::Restriction::IO(3User Contributed Perl DocumentatiBio::Restriction::IO(3)NAMEBio::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
DESCRIPTIONBio::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:
http://bugzilla.open-bio.org/
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
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 v5.14.1 2011-07-22 Bio::Restriction::IO(3)
