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://redmine.open-bio.org/projects/bioperl/
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
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :