Difference between revisions of "Proxy"

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==Example==
 
==Example==
This script combines two [[CalcInterSubfeatures|CalcInterSubfeatures]] modules with a '''FilterSubfeatures''' module to manipulate a complex gene model of exons and UTRs into a new gene model based on coding exons. It first creates ''intron'' features between the exons which might 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 '''FilterSubfeatures''' rebuilds the transcript gene model using only these ''codingexon'' subfeatures.
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This is a script which incorporates a '''Proxy''' / [[TemplateCluster|TemplateCluster]] to collate expression into Gencode V10 gene models. The expression is then normalized via the[[NormalizeRPKM|NormalizeRPKM]] module. The script finishes with [[CalcFeatureSignificance|CalcFeatureSignificance]] so that the Features can be displayed via score-coloring.
  
 
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Revision as of 19:37, 15 May 2012

Description

The FilterSubfeatures processing module is designed to work on Features with subfeatures to remove subfeatures not specified in the category filtering and then rebuild the outer feature boundaries based on the remaining subfeatures. The module will resort features on the data stream as needed to preserve the stream integrity.

Atributes

Proxy is a special module in the system and does not have parameters. Instead it has a single attribute

  • name : name of the <datastream> which will be injected in place of this proxy at query time.

Example

This is a script which incorporates a Proxy / TemplateCluster to collate expression into Gencode V10 gene models. The expression is then normalized via theNormalizeRPKM module. The script finishes with CalcFeatureSignificance so that the Features can be displayed via score-coloring.

<zenbu_script>
	<datastream name="gencode">
		<source id="D71B7748-1450-4C62-92CB-7E913AB12899::19:::FeatureSource"/>
	</datastream>
	<stream_queue>
		<spstream module="TemplateCluster">
			<overlap_mode>height</overlap_mode>
			<skip_empty_templates>false</skip_empty_templates>
			<expression_mode>sum</expression_mode>
			<overlap_subfeatures>true</overlap_subfeatures>
			<ignore_strand>true</ignore_strand>
			<side_stream>
				<spstream module="EEDB::SPStream::Proxy" name="gencode"/>
			</side_stream>
		</spstream>

		<spstream module="NormalizeRPKM"/>

		<spstream module="CalcFeatureSignificance"/>
	</stream_queue>
</zenbu_script>

Here is a ZENBU view showing this script in use
http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=vtPXLwwqO9KjD1YYWqCMGD;loc=hg19::chr8:128746973..128755020