/ 
bioperl-1.4
/ Bio::Restriction::IO

NAME

Bio::Restriction::IO - Handler for sequence variation IO Formats

SYNOPSIS

  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>;

DESCRIPTION

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.

TO DO

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.

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://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/

AUTHOR

Rob Edwards, redwards@utmem.edu

CONTRIBUTORS

Heikki Lehvaslaiho, heikki@ebi.ac.uk

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    :