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1 package edu.unc.genomics.ngs;
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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.io.IntervalFile;
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19
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20 public class RollingReadLength extends CommandLineTool {
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21
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22 private static final Logger log = Logger.getLogger(RollingReadLength.class);
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23
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24 @Parameter(names = {"-i", "--input"}, description = "Input file (reads)", required = true)
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25 public IntervalFile<? extends Interval> intervalFile;
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26 @Parameter(names = {"-a", "--assembly"}, description = "Genome assembly", required = true)
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27 public Assembly assembly;
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28 @Parameter(names = {"-o", "--output"}, description = "Output file (Wig)", required = true)
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29 public Path outputFile;
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30
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31 @Override
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32 public void run() throws IOException {
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33 log.debug("Initializing output file");
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34 int mapped = 0;
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35 try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
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36 // Write the Wiggle track header to the output file
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37 TrackHeader header = new TrackHeader("wiggle_0");
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38 header.setName("Converted " + intervalFile.getPath().getFileName());
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39 header.setDescription("Converted " + intervalFile.getPath().getFileName());
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40 writer.write(header.toString());
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41 writer.newLine();
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42
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43 // Process each chromosome in the assembly
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44 for (String chr : assembly) {
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45 log.debug("Processing chromosome " + chr);
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46 // Write the contig header to the output file
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47 writer.write("fixedStep chrom="+chr+" start=1 step=1 span=1");
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48 writer.newLine();
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49
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50 int start = 1;
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51 while (start < assembly.getChrLength(chr)) {
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52 int stop = start + DEFAULT_CHUNK_SIZE - 1;
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53 int length = stop - start + 1;
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54 int[] sum = new int[length];
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55 int[] count = new int[length];
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56
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57 Iterator<? extends Interval> it = intervalFile.query(chr, start, stop);
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58 while (it.hasNext()) {
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59 Interval entry = it.next();
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60 for (int i = entry.getStart(); i <= entry.getStop(); i++) {
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61 sum[i-start] += entry.length();
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62 count[i-start]++;
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63 }
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64 mapped++;
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65 }
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66
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67 // Write the average at each base pair to the output file
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68 for (int i = 0; i < sum.length; i++) {
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69 if (count[i] == 0) {
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70 writer.write(String.valueOf(Float.NaN));
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71 } else {
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72 writer.write(String.valueOf(sum[i]/count[i]));
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73 }
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74 writer.newLine();
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75 }
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76
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77 // Process the next chunk
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78 start = stop + 1;
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79 }
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80 }
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81 }
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82
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83 log.info("Mapped "+mapped+" reads");
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84 }
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85
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86 public static void main(String[] args) {
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87 new RollingReadLength().instanceMain(args);
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88 }
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89 } |
