The SteramSubfeatures processing module is designed to work on Features with subfeatures and exports them onto the primary data stream. The subfeatures can be selected based on their category. In addition there are parameter control options related to expression and uniquing.
- <category_filter> : defines the subfeatures which are exported from the primary feature.
- <transfer_expression> : if true the expression from the primary Feature is transfered to all the subfeatures equally using the height expression method described in TemplateCluster.
- <unique> : internall implements the same algorithm as the UniqueFeature module.
This script combines two CalcInterSubfeatures modules with a StreamSubfeatures module to manipulate a complex gene model of exons and UTRs into an exported set of coding exons. It first creates intron features between the exons which can be labeled either as block or exon. The second CalcInterSubfeatures then uses 5utr and 3utr and intron as demarkation to create codingexon subfeatures. Lastly the StreamSubfeatures exports these codingexon subfeatures out onto the primary data stream.
<zenbu_script> <stream_queue> <spstream module="CalcInterSubfeatures"> <category_filter>block</category_filter> <category_filter>exon</category_filter> <new_subfeature_category>intron</new_subfeature_category> </spstream> <spstream module="CalcInterSubfeatures"> <category_filter>5utr</category_filter> <category_filter>3utr</category_filter> <category_filter>intron</category_filter> <new_subfeature_category>codingexon</new_subfeature_category> </spstream> <spstream module="StreamSubfeatures"> <category_filter>codingexon</category_filter> <transfer_expression>true</transfer_expression> </spstream> </stream_queue> </zenbu_script>
Here is a ZENBU view showing this script in use