Difference between revisions of "Proxy"

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(Example)
(Description)
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==Description==
 
==Description==
The '''FilterSubfeatures''' [[DataProcessing#Processing_modules|processing module]] is designed to work on [[DataModel#Feature|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.
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The '''Proxy''' a special splace holder [[DataProcessing#Processing_modules|processing module]] is designed to work in coordination with the <datasources> section of the ZENBU scripting system. By separating the data sources and proxy it is possible to provide security checking of access to the datasources and allows the pooled datasources to be reused in different sections of the same script.
  
 
==Atributes==
 
==Atributes==

Revision as of 19:39, 15 May 2012

Description

The Proxy a special splace holder processing module is designed to work in coordination with the <datasources> section of the ZENBU scripting system. By separating the data sources and proxy it is possible to provide security checking of access to the datasources and allows the pooled datasources to be reused in different sections of the same script.

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