FeatureLengthFilter

Data Stream Processing > Processing Modules > Filtering Modules

Description

The FeatureLengthFilter processing module is designed to filter Features based on their length. The module is configurable with both a min_length and/or max_length. If only min_length is specified it will act as a high-pass filter. If only max_length is specified it will act as a low-pass filter. If both min_length and max_length are specified it will act as a band-pass filter.

Parameters

• <min_length> : Features smaller than min_length are filtered out.
• <max_length> : Features larger than max_length are filtered out.

Example

This is a complex script which incorporates a FeatureEmitter / TemplateCluster expression histogram binning with de-novo clustering via Paraclu followed by several filtering steps including NeighborCutoff, CutoffFilter, and a final FeatureLengthFilter to remove very tiny clusters.

<zenbu_script>
	<stream_queue>
		<spstream module="TemplateCluster">
			<overlap_mode>area</overlap_mode>
			<expression_mode>sum</expression_mode>
			<side_stream>
				<spstream module="FeatureEmitter">
					<width>1</width>
					<fixed_grid>true</fixed_grid>
					<both_strands>true</both_strands>
				</spstream>
			</side_stream>
		</spstream>

		<spstream module="Paraclu">
			<min_cutoff>10</min_cutoff>
			<stability>0</stability>
			<max_cluster_length>100</max_cluster_length>
		</spstream>

		<spstream module="CalcFeatureSignificance"/>

		<spstream module="NeighborCutoff">
			<ratio>300</ratio>
			<distance>100</distance>
		</spstream>

		<spstream module="CutoffFilter">
			<min_cutoff>100</min_cutoff>
		</spstream>

		<spstream module="FeatureLengthFilter">
			<max_length>50</max_length>
		</spstream>

	</stream_queue>
</zenbu_script>

Example ZENBU view showing this script in use
http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=jqr7D6J2PxMrOdqTg8glvD;loc=hg19::chr19:49990236..49997699