Mercurial > repos > timpalpant > java_genomics_toolkit

comparison src/edu/unc/genomics/wigmath/Average.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.nio.file.Paths;
5 import java.util.ArrayList;
6 import java.util.Iterator;
7 import java.util.List;
8
9 import org.apache.log4j.Logger;
10 import org.broad.igv.bbfile.WigItem;
11
12 import com.beust.jcommander.Parameter;
13
14 import edu.unc.genomics.CommandLineToolException;
15 import edu.unc.genomics.io.WigFile;
16 import edu.unc.genomics.io.WigFileException;
17
18 public class Average extends WigMathTool {
19
20 private static final Logger log = Logger.getLogger(Average.class);
21
22 @Parameter(description = "Input files", required = true)
23 public List<String> inputFiles = new ArrayList<String>();
24
25 int numFiles;
26
27 @Override
28 public void setup() {
29 if (inputFiles.size() < 2) {
30 throw new CommandLineToolException("No reason to add < 2 files.");
31 }
32
33 log.debug("Initializing input files");
34 for (String inputFile : inputFiles) {
35 try {
36 addInputFile(WigFile.autodetect(Paths.get(inputFile)));
37 } catch (IOException | WigFileException e) {
38 log.error("Error initializing input Wig file: " + inputFile);
39 e.printStackTrace();
40 throw new CommandLineToolException(e.getMessage());
41 }
42 }
43 log.debug("Initialized " + inputs.size() + " input files");
44
45 numFiles = inputs.size();
46 }
47
48 @Override
49 public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
50 log.debug("Computing average for chunk "+chr+":"+start+"-"+stop);
51
52 int length = stop - start + 1;
53 float[] avg = new float[length];
54
55 for (WigFile wig : inputs) {
56 Iterator<WigItem> data = wig.query(chr, start, stop);
57 while (data.hasNext()) {
58 WigItem item = data.next();
59 for (int i = item.getStartBase(); i <= item.getEndBase(); i++) {
60 if (i-start >= 0 && i-start < avg.length) {
61 avg[i-start] += item.getWigValue();
62 }
63 }
64 }
65 }
66
67 for (int i = 0; i < avg.length; i++) {
68 avg[i] = avg[i] / numFiles;
69 }
70
71 return avg;
72 }
73
74
75 /**
76 * @param args
77 * @throws WigFileException
78 * @throws IOException
79 */
80 public static void main(String[] args) throws IOException, WigFileException {
81 new Average().instanceMain(args);
82 }
83
84 }