NAME

Bio::SeqIO::game - Parses GAME XML 0.1 and higher into and out of Bio::Seq objects.

SYNOPSIS

To use this module you need XML::Parser, XML::Parser::PerlSAX and XML::Writer.

Do not use this module directly. Use it via the Bio::SeqIO class.

DESCRIPTION

This object can transform Bio::Seq objects to and from bioxml seq, computation, feature and annotation dtds,versions 0.1 and higher. These can be found at http://www.bioxml.org/dtds/current. It does this using the idHandler, seqHandler and featureHandler modules you should have gotten with this one.

The idea is that any bioxml features can be turned into bioperl annotations. When Annotations and computations are parsed in, they gain additional info in the bioperl SeqFeature tag attribute. These can be used to reconstitute a computation or annotation by the bioxml with the bx-handler module when write_seq is called.

If you use this to write SeqFeatures that were not generated from computations or annotations, it will output a list of bioxml features. Some data may be lost in this step, since bioxml features just have a span, type and description - nothing about the anlysis performed.

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 one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org        - Technical bioperl discussion
  bioxml-dev@bioxml.org        - Technical discussion - Moderate volume
  bioxml-announce@bioxml.org   - General Announcements - Pretty dead
  http://www.bioxml.org/MailingLists/         - About the mailing lists

AUTHOR - Brad Marshall & Ewan Birney & Lincoln Stein

Email: bradmars@yahoo.com birney@sanger.ac.uk lstein@cshl.org

CONTRIBUTORS

Jason Stajich <jason@bioperl.org>

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

_export_subfeatures

 Title   : _export_subfeatures
 Usage   : $obj->_export_subfeatures
 Function: export all subfeatures (also in the geneprediction structure)
 Returns : value of _export_subfeatures
 Args    : newvalue (optional)

_group_subfeatures

 Title   : _group_subfeatures
 Usage   : $obj->_group_subfeatures
 Function: Groups all subfeatures in separate feature_sets
 Returns : value of _group_subfeatures
 Args    : newvalue (optional)

_subfeature_types

 Title   : _subfeature_types
 Usage   : $obj->_subfeature_types
 Function: array of all possible subfeatures, it should be a 
           name of a function which
         : returns an arrau of sub_seqfeatures when called: 
           @array = $feature->subfeaturetype()
 Returns : array of _subfeature_types
 Args    : array of subfeature types (optional)

_add_subfeature_type

 Title   : _add_subfeature_type
 Usage   : $obj->_add_subfeature_type
 Function: add one possible subfeature, it should be a name of a function which
         : returns an arrau of sub_seqfeatures when called: @array = $feature->subfeaturetyp()
 Returns : 1
 Args    : one subfeature type (optional)

next_seq

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    : NONE

next_primary_seq

 Title   : next_primary_seq
 Usage   : $seq = $stream->next_primary_seq()
 Function: returns the next primary sequence (ie no seq_features) in the stream
 Returns : Bio::PrimarySeq object
 Args    : NONE

write_seq

 Title   : write_seq
 Usage   : Not Yet Implemented! $stream->write_seq(@seq)
 Function: writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Seq object