Bio::Restriction::IO - Handler for sequence variation IO Formats
$in = Bio::Restriction::IO->new(-file => "inputfilename" ,
-format => 'withrefm');
my $res = $in->read; # a Bio::Restriction::EnzymeCollection
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
For more details, see documentation in Bio::SeqIO.
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 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)?
Bio::SeqIO, Bio::Restriction::Enzyme, Bio::Restriction::EnzymeCollection
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The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
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
Title : format
Usage : $format = $stream->format()
Function: Get the restriction format
Returns : restriction format
Args : none
Title : read
Usage : $renzs = $stream->read
Function: reads all the restrction enzymes from the stream
Returns : a Bio::Restriction::EnzymeCollection object
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)
Returns : guessed format of filename (lower case)