Summary

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

Package variables

Inherit

Bio::SeqIO

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.

Methods

Methods description

 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   : read
 Usage   : $renzs = $stream->read
 Function: reads all the restrction enzymes from the stream
 Returns : a Bio::Restriction::EnzymeCollection object
 Args    :

 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    :

Methods code

sub new {

   my ($class, %param) = @_;
   my ($format);

   @param{ map { lc $_ } keys %param } = values %param;  # lowercase keys
   $format = $FORMAT{$param{'-format'}} if defined $param{'-format'};
   $format ||= $class->_guess_format( $param{-file} || $ARGV[0] )
             || 'base';
   $format = "\L$format"; # normalize capitalization to lower case

   return unless $class->_load_format_module($format);
   return "Bio::Restriction::IO::$format"->new(%param);

}

sub _load_format_module {

  my ($class, $format) = @_;
  my $module = "Bio::Restriction::IO::" . $format;
  my $ok;
  eval {
      $ok = $class->_load_module($module);
  };
  if ( $@ ) {
    print STDERR <<END;
$class: $format cannot be found
Exception $@
For more information about the IO system please see the IO docs.
This includes ways of checking for formats at compile time, not run time
END
  ;
  }
  return $ok;

}

sub read {

   my ($self, $seq) = @_;
   $self->throw_not_implemented();

}

sub next {

   my ($self, $seq) = @_;
   $self->throw_not_implemented();

}

sub next_seq {

   my ($self, $seq) = @_;
   $self->throw_not_implemented();

}

sub write {

    my ($self, $seq) = @_;
    $self->throw("Sorry, you cannot write to a generic ".
                 "Bio::Restricion::IO object.");

}

sub write_seq {

   my ($self, $seq) = @_;
   $self->warn("These are not sequence objects. ".
               "Use method 'write' instead of 'write_seq'.");
   $self->write($seq);

}

sub _guess_format {

   my $class = shift;
   return  unless $_ = shift;
   return 'flat' if /\.dat$/i;
   return 'xml'  if /\.xml$/i;
}


1;

}

General documentation

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)?

Bio::SeqIO,
Bio::Restriction::Enzyme,
Bio::Restriction::EnzymeCollection

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

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:

  http://bugzilla.open-bio.org/

Rob Edwards, redwards@utmem.edu

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 _