Manual Reference Pages - BIO::RESTRICTION::IO (3)
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 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)?
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.
email@example.com - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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
Rob Edwards, firstname.lastname@example.org
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
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)
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