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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.ArrayList;
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9 import java.util.Collections;
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10 import java.util.HashMap;
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11 import java.util.List;
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12 import java.util.Map;
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13
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14 import org.apache.log4j.Logger;
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15
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16 import com.beust.jcommander.Parameter;
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17
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18 import edu.unc.genomics.CommandLineTool;
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19 import edu.unc.genomics.Interval;
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20 import edu.unc.genomics.ReadablePathValidator;
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21 import edu.unc.genomics.io.IntervalFile;
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22
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23 public class FindBoundaryNucleosomes extends CommandLineTool {
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24
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25 private static final Logger log = Logger.getLogger(FindBoundaryNucleosomes.class);
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26
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27 @Parameter(names = {"-i", "--input"}, description = "Input file (nucleosome calls)", required = true, validateWith = ReadablePathValidator.class)
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28 public Path inputFile;
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29 @Parameter(names = {"-l", "--loci"}, description = "Boundary loci (Bed format)", required = true)
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30 public IntervalFile<? extends Interval> lociFile;
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31 @Parameter(names = {"-o", "--output"}, description = "Output file", required = true)
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32 public Path outputFile;
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33
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34 private Map<String,List<NucleosomeCall>> nucs = new HashMap<>();
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35
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36 private List<NucleosomeCall> getIntervalNucleosomes(Interval i) {
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37 List<NucleosomeCall> intervalNucs = new ArrayList<>();
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38 for (NucleosomeCall call : nucs.get(i.getChr())) {
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39 if (call.getDyad() >= i.low() && call.getDyad() <= i.high()) {
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40 intervalNucs.add(call);
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41 }
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42 }
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43
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44 return intervalNucs;
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45 }
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46
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47 @Override
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48 public void run() throws IOException {
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49 log.debug("Initializing input file");
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50 NucleosomeCallsFile nucsFile = new NucleosomeCallsFile(inputFile);
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51 log.debug("Loading all nucleosomes");
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52 for (NucleosomeCall nuc : nucsFile) {
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53 if (nuc == null) continue;
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54 if (!nucs.containsKey(nuc.getChr())) {
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55 nucs.put(nuc.getChr(), new ArrayList<NucleosomeCall>());
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56 }
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57 nucs.get(nuc.getChr()).add(nuc);
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58 }
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59 nucsFile.close();
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60
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61 log.debug("Initializing output file");
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62 int skipped = 0;
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63 try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
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64 log.debug("Finding boundary nucleosomes for each interval");
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65 NucleosomeCall.DyadComparator comparator = new NucleosomeCall.DyadComparator();
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66 for (Interval interval : lociFile) {
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67 writer.write(interval.toBed());
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68
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69 // Get all of the nucleosomes within this interval
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70 List<NucleosomeCall> intervalNucs = getIntervalNucleosomes(interval);
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71
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72 if (intervalNucs.size() > 0) {
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73 // Sort the list by nucleosome position
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74 Collections.sort(intervalNucs, comparator);
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75 if (interval.isCrick()) {
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76 Collections.reverse(intervalNucs);
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77 }
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78
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79 int fivePrime = intervalNucs.get(0).getDyad();
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80 int threePrime = intervalNucs.get(intervalNucs.size()-1).getDyad();
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81 writer.write("\t"+fivePrime+"\t"+threePrime);
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82 } else {
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83 skipped++;
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84 writer.write("\tNA\tNA");
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85 }
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86
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87 writer.newLine();
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88 }
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89 }
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90
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91 lociFile.close();
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92 log.info("Skipped "+skipped+" intervals with 0 nucleosomes");
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93 }
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94
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95 public static void main(String[] args) {
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96 new FindBoundaryNucleosomes().instanceMain(args);
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97 }
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98 } |
