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