Mercurial > repos > timpalpant > java_genomics_toolkit
diff src/edu/unc/genomics/wigmath/MovingAverageSmooth.java @ 2:e16016635b2a
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author | timpalpant |
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date | Mon, 13 Feb 2012 22:12:06 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/edu/unc/genomics/wigmath/MovingAverageSmooth.java Mon Feb 13 22:12:06 2012 -0500 @@ -0,0 +1,67 @@ +package edu.unc.genomics.wigmath; + +import java.io.IOException; +import java.util.Iterator; + +import org.apache.commons.math.stat.descriptive.DescriptiveStatistics; +import org.apache.log4j.Logger; +import org.broad.igv.bbfile.WigItem; + +import com.beust.jcommander.Parameter; + +import edu.unc.genomics.PositiveIntegerValidator; +import edu.unc.genomics.io.WigFile; +import edu.unc.genomics.io.WigFileException; + +public class MovingAverageSmooth extends WigMathTool { + + private static final Logger log = Logger.getLogger(MovingAverageSmooth.class); + + @Parameter(names = {"-i", "--input"}, description = "Input file", required = true) + public WigFile inputFile; + @Parameter(names = {"-w", "--width"}, description = "Width of kernel (bp)") + public int width = 10; + + WigFile input; + DescriptiveStatistics stats; + + @Override + public void setup() { + inputs.add(inputFile); + + log.debug("Initializing statistics"); + stats = new DescriptiveStatistics(); + stats.setWindowSize(width); + } + + @Override + public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { + log.debug("Smoothing chunk "+chr+":"+start+"-"+stop); + // Pad the query so that we can provide values for the ends + int queryStart = Math.max(start-width/2, input.getChrStart(chr)); + int queryStop = Math.min(stop+width/2, input.getChrStop(chr)); + Iterator<WigItem> result = input.query(chr, queryStart, queryStop); + float[] data = WigFile.flattenData(result, queryStart, queryStop); + + float[] smoothed = new float[stop-start+1]; + for (int bp = start; bp <= stop; bp++) { + stats.addValue(data[bp-queryStart]); + if (bp-start-width/2 >= 0) { + smoothed[bp-start-width/2] = (float) stats.getMean(); + } + } + + return smoothed; + } + + + /** + * @param args + * @throws WigFileException + * @throws IOException + */ + public static void main(String[] args) throws IOException, WigFileException { + new MovingAverageSmooth().instanceMain(args); + } + +}