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.
bioxml-dev@bioxml.org - Technical discussion - Moderate volume
bioxml-announce@bioxml.org - General Announcements - Pretty dead
http://www.bioxml.org/MailingLists/ - About the mailing listsAUTHOR - Brad Marshall & Ewan Birney & Lincoln Stein
Email: bradmars@yahoo.com birney@sanger.ac.uk lstein@cshl.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->subfeaturetyp()
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 : NONEnext_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 : NONEwrite_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