Bio::Restriction IO
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Summary
Bio::Restriction::IO - Handler for sequence variation IO Formats
Package variables
No package variables defined.
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
newDescriptionCode
_load_format_module
No description
Code
readDescriptionCode
next
No description
Code
next_seq
No description
Code
writeDescriptionCode
write_seq
No description
Code
_guess_formatDescriptionCode
Methods description
newcode    nextTop
 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
readcodeprevnextTop
 Title   : read
Usage : $renzs = $stream->read
Function: reads all the restrction enzymes from the stream
Returns : a Bio::Restriction::EnzymeCollection object
Args :
writecodeprevnextTop
 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_formatcodeprevnextTop
 Title   : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
Methods code
newdescriptionprevnextTop
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::$format"->new(%param);
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
  my ($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 $ok;
}
readdescriptionprevnextTop
sub read {
   my ($self, $seq) = @_;
   $self->throw_not_implemented();
}
nextdescriptionprevnextTop
sub next {
   my ($self, $seq) = @_;
   $self->throw_not_implemented();
}
next_seqdescriptionprevnextTop
sub next_seq {
   my ($self, $seq) = @_;
   $self->throw_not_implemented();
}
writedescriptionprevnextTop
sub write {
    my ($self, $seq) = @_;
    $self->throw("Sorry, you cannot write to a generic ".
                 "Bio::Restricion::IO object.");
}
write_seqdescriptionprevnextTop
sub write_seq {
   my ($self, $seq) = @_;
   $self->warn("These are not sequence objects. ".
               "Use method 'write' instead of 'write_seq'.");
   $self->write($seq);
}
_guess_formatdescriptionprevnextTop
sub _guess_format {
   my $class = shift;
   return  unless $_ = shift;
   return 'flat' if /\.dat$/i;
   return 'xml'  if /\.xml$/i;
}


1;
}
General documentation
TO DOTop
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)?
SEE ALSOTop
Bio::SeqIO,
Bio::Restriction::Enzyme,
Bio::Restriction::EnzymeCollection
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
Reporting BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Rob Edwards, redwards@utmem.edu
CONTRIBUTORSTop
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
formatTop
 Title   : format
Usage : $format = $stream->format()
Function: Get the restriction format
Returns : restriction format
Args : none