Mercurial > repos > timpalpant > java_genomics_toolkit
comparison 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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1:a54db233ee3d | 2:e16016635b2a |
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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 } |