Mercurial > repos > timpalpant > java_genomics_toolkit

comparison java-genomics-toolkit/src/edu/unc/genomics/nucleosomes/Phasogram.java @ 0:1daf3026d231

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author timpalpant
date Mon, 13 Feb 2012 21:55:55 -0500
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1 package edu.unc.genomics.nucleosomes;
2
3 import java.io.BufferedWriter;
4 import java.io.IOException;
5 import java.nio.charset.Charset;
6 import java.nio.file.Files;
7 import java.nio.file.Path;
8
9 import org.apache.log4j.Logger;
10
11 import com.beust.jcommander.Parameter;
12
13 import edu.unc.genomics.CommandLineTool;
14 import edu.unc.genomics.CommandLineToolException;
15 import edu.unc.genomics.io.WigFile;
16 import edu.unc.genomics.io.WigFileException;
17
18 public class Phasogram extends CommandLineTool {
19
20 private static final Logger log = Logger.getLogger(Phasogram.class);
21
22 @Parameter(names = {"-i", "--input"}, description = "Input wig file (read counts)", required = true)
23 public WigFile inputFile;
24 @Parameter(names = {"-m", "--max"}, description = "Maximum phase shift", required = true)
25 public int maxPhase;
26 @Parameter(names = {"-o", "--output"}, description = "Output file (histogram)", required = true)
27 public Path outputFile;
28
29 public void run() throws IOException {
30 long[] phaseCounts = new long[maxPhase+1];
31
32 // Process each chromosome in the assembly
33 for (String chr : inputFile.chromosomes()) {
34 log.debug("Processing chromosome " + chr);
35
36 int start = inputFile.getChrStart(chr);
37 while (start < inputFile.getChrStop(chr)) {
38 int stop = start + DEFAULT_CHUNK_SIZE - 1;
39
40 try {
41 float[] data = WigFile.flattenData(inputFile.query(chr, start, stop), start, stop);
42 for (int i = 0; i < data.length-maxPhase; i++) {
43 for (int j = 0; j <= maxPhase; j++) {
44 phaseCounts[j] += data[i];
45 }
46 }
47
48 } catch (WigFileException e) {
49 log.fatal("Error querying data from Wig file!");
50 e.printStackTrace();
51 throw new CommandLineToolException("Error querying data from Wig file!");
52 }
53
54 // Process the next chunk
55 start = stop - maxPhase + 1;
56 }
57 }
58
59 log.debug("Writing output to disk");
60 try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
61 for (int i = 0; i < phaseCounts.length; i++) {
62 writer.write(i+"\t"+phaseCounts[i]);
63 writer.newLine();
64 }
65 }
66 }
67
68 public static void main(String[] args) {
69 new Phasogram().instanceMain(args);
70 }
71 }