Mercurial > repos > timpalpant > java_genomics_toolkit

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

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author timpalpant
date Mon, 13 Feb 2012 22:12:06 -0500
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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.log4j.Logger;
7 import org.broad.igv.bbfile.WigItem;
8
9 import com.beust.jcommander.Parameter;
10
11 import edu.unc.genomics.CommandLineToolException;
12 import edu.unc.genomics.io.WigFile;
13 import edu.unc.genomics.io.WigFileException;
14
15 public class ZScore extends WigMathTool {
16
17 private static final Logger log = Logger.getLogger(ZScore.class);
18
19 @Parameter(names = {"-i", "--input"}, description = "Input file", required = true)
20 public WigFile inputFile;
21
22 double mean;
23 double stdev;
24
25 @Override
26 public void setup() {
27 inputs.add(inputFile);
28
29 mean = inputFile.mean();
30 stdev = inputFile.stdev();
31 if(stdev == 0) {
32 log.error("Cannot Z-score a file with stdev = 0!");
33 throw new CommandLineToolException("Cannot Z-score a file with stdev = 0!");
34 }
35 }
36
37 @Override
38 public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
39 log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop);
40 Iterator<WigItem> data = inputFile.query(chr, start, stop);
41 float[] result = WigFile.flattenData(data, start, stop);
42
43 for (int i = 0; i < result.length; i++) {
44 result[i] = (float)((result[i] - mean) / stdev);
45 }
46
47 return result;
48 }
49
50
51 /**
52 * @param args
53 * @throws WigFileException
54 * @throws IOException
55 */
56 public static void main(String[] args) throws IOException, WigFileException {
57 new ZScore().instanceMain(args);
58 }
59
60 }