- AUTHOR - Brad Marshall & Ewan Birney & Lincoln Stein
Bio::SeqIO::game - Parses GAME XML 0.1 and higher into and out of Bio::Seq objects.
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.
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.
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : _export_subfeatures Usage : $obj->_export_subfeatures Function: export all subfeatures (also in the geneprediction structure) Returns : value of _export_subfeatures Args : newvalue (optional)
Title : _group_subfeatures Usage : $obj->_group_subfeatures Function: Groups all subfeatures in separate feature_sets Returns : value of _group_subfeatures Args : newvalue (optional)
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)
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)
Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : NONE
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
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