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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 import java.util.Iterator;
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9
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10 import org.apache.log4j.Logger;
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11
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12 import com.beust.jcommander.Parameter;
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13
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14 import edu.ucsc.genome.TrackHeader;
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15 import edu.unc.genomics.Assembly;
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16 import edu.unc.genomics.CommandLineTool;
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17 import edu.unc.genomics.Interval;
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18 import edu.unc.genomics.PositiveIntegerValidator;
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19 import edu.unc.genomics.io.IntervalFile;
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20
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21 public class MapDyads extends CommandLineTool {
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22
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23 private static final Logger log = Logger.getLogger(MapDyads.class);
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24
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25 @Parameter(names = {"-i", "--input"}, description = "Input file (reads)", required = true)
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26 public IntervalFile<? extends Interval> inputFile;
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27 @Parameter(names = {"-s", "--size"}, description = "Mononucleosome length (default: read length)", validateWith = PositiveIntegerValidator.class)
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28 public Integer nucleosomeSize;
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29 @Parameter(names = {"-a", "--assembly"}, description = "Genome assembly", required = true)
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30 public Assembly assembly;
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31 @Parameter(names = {"-o", "--output"}, description = "Output file (Wig)", required = true)
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32 public Path outputFile;
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33
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34 @Override
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35 public void run() throws IOException {
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36 log.debug("Initializing output file");
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37 int mapped = 0;
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38 try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
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39 // Write the Wiggle track header to the output file
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40 TrackHeader header = new TrackHeader("wiggle_0");
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41 header.setName("Converted " + inputFile.getPath().getFileName());
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42 header.setDescription("Converted " + inputFile.getPath().getFileName());
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43 writer.write(header.toString());
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44 writer.newLine();
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45
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46 // Process each chromosome in the assembly
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47 for (String chr : assembly) {
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48 log.debug("Processing chromosome " + chr);
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49 // Write the contig header to the output file
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50 writer.write("fixedStep chrom="+chr+" start=1 step=1 span=1");
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51 writer.newLine();
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52
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53 int start = 1;
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54 while (start < assembly.getChrLength(chr)) {
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55 int stop = start + DEFAULT_CHUNK_SIZE - 1;
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56 int length = stop - start + 1;
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57 int[] count = new int[length];
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58
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59 Iterator<? extends Interval> it = inputFile.query(chr, start, stop);
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60 while (it.hasNext()) {
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61 Interval entry = it.next();
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62 if (nucleosomeSize == null) {
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63 count[entry.center()-start]++;
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64 } else {
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65 count[entry.getStart()+nucleosomeSize-start]++;
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66 }
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67 mapped++;
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68 }
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69
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70 // Write the average at each base pair to the output file
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71 for (int i = 0; i < count.length; i++) {
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72 writer.write(count[i]);
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73 writer.newLine();
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74 }
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75
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76 // Process the next chunk
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77 start = stop + 1;
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78 }
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79 }
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80 }
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81
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82 log.info("Mapped "+mapped+" reads");
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83 }
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84
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85 public static void main(String[] args) {
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86 new MapDyads().instanceMain(args);
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87 }
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88 } |
