Bio::Restriction::IO - Handler for sequence variation IO Formats use Bio::Restriction::IO; $in = Bio::Restriction::IO->new(-file => "inputfilename" , -format => 'withrefm'); $out = Bio::Restriction::IO->new(-file => ">outputfilename" , -format => 'bairoch'); my $res = $in->read; # a Bio::Restriction::EnzymeCollection $out->write($res); # or # use Bio::Restriction::IO; # # #input file format can be read from the file extension (dat|xml) # $in = Bio::Restriction::IO->newFh(-file => "inputfilename"); # $out = Bio::Restriction::IO->newFh('-format' => 'xml'); # # # World's shortest flat<->xml format converter: # print $out $_ while <$in>; Bio::Restriction::IO is a handler module for the formats in the Restriction IO set (eg, 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 module. The main difference is that instead of using methods next_seq and write_seq, you drop '_seq' from the method names. Also, instead of dealing only with individual Bio::Restriction::Enzyme objects, write() will go through all enzymes from a Bio::Restriction::EnzymeCollection objects and read() will slurp in all enzymes into a Collection. For more details, see documentation in Bio::SeqIO. This inherits from SeqIOfor convinience sake. Get rid of it by copying relevant methods in. Bio::SeqIO has too many sequence IO specific tweeks in it. Bio::SeqIO, Bio::Restriction::Enzyme, Bio::Restriction::EnzymeCollection

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Rob Edwards, redwards@utmem.edu Heikki Lehvaslaiho, heikki@ebi.ac.uk 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 :