Mercurial > repos > timpalpant > java_genomics_toolkit

comparison src/edu/unc/genomics/wigmath/MovingAverageSmooth.java @ 2:e16016635b2a

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author timpalpant
date Mon, 13 Feb 2012 22:12:06 -0500
parents
children
comparison
equal deleted inserted replaced
1:a54db233ee3d 2:e16016635b2a
1 package edu.unc.genomics.wigmath;
2
3 import java.io.IOException;
4 import java.util.Iterator;
5
6 import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;
7 import org.apache.log4j.Logger;
8 import org.broad.igv.bbfile.WigItem;
9
10 import com.beust.jcommander.Parameter;
11
12 import edu.unc.genomics.PositiveIntegerValidator;
13 import edu.unc.genomics.io.WigFile;
14 import edu.unc.genomics.io.WigFileException;
15
16 public class MovingAverageSmooth extends WigMathTool {
17
18 private static final Logger log = Logger.getLogger(MovingAverageSmooth.class);
19
20 @Parameter(names = {"-i", "--input"}, description = "Input file", required = true)
21 public WigFile inputFile;
22 @Parameter(names = {"-w", "--width"}, description = "Width of kernel (bp)")
23 public int width = 10;
24
25 WigFile input;
26 DescriptiveStatistics stats;
27
28 @Override
29 public void setup() {
30 inputs.add(inputFile);
31
32 log.debug("Initializing statistics");
33 stats = new DescriptiveStatistics();
34 stats.setWindowSize(width);
35 }
36
37 @Override
38 public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
39 log.debug("Smoothing chunk "+chr+":"+start+"-"+stop);
40 // Pad the query so that we can provide values for the ends
41 int queryStart = Math.max(start-width/2, input.getChrStart(chr));
42 int queryStop = Math.min(stop+width/2, input.getChrStop(chr));
43 Iterator<WigItem> result = input.query(chr, queryStart, queryStop);
44 float[] data = WigFile.flattenData(result, queryStart, queryStop);
45
46 float[] smoothed = new float[stop-start+1];
47 for (int bp = start; bp <= stop; bp++) {
48 stats.addValue(data[bp-queryStart]);
49 if (bp-start-width/2 >= 0) {
50 smoothed[bp-start-width/2] = (float) stats.getMean();
51 }
52 }
53
54 return smoothed;
55 }
56
57
58 /**
59 * @param args
60 * @throws WigFileException
61 * @throws IOException
62 */
63 public static void main(String[] args) throws IOException, WigFileException {
64 new MovingAverageSmooth().instanceMain(args);
65 }
66
67 }