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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.nio.file.Paths;
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9 import java.util.ArrayList;
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10 import java.util.Iterator;
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11 import java.util.List;
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12
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13 import org.apache.log4j.Logger;
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14 import org.broad.igv.bbfile.WigItem;
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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.io.IntervalFile;
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21 import edu.unc.genomics.io.WigFile;
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22 import edu.unc.genomics.io.WigFileException;
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23
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24 public class FindAbsoluteMaxima extends CommandLineTool {
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25
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26 private static final Logger log = Logger.getLogger(FindAbsoluteMaxima.class);
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27
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28 @Parameter(description = "Input files", required = true)
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29 public List<String> inputFiles = new ArrayList<String>();
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30 @Parameter(names = {"-l", "--loci"}, description = "Loci file (Bed)", required = true)
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31 public IntervalFile<? extends Interval> lociFile;
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32 @Parameter(names = {"-o", "--output"}, description = "Output file", required = true)
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33 public Path outputFile;
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34
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35 private List<WigFile> wigs = new ArrayList<>();
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36
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37 @Override
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38 public void run() throws IOException {
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39 log.debug("Initializing input Wig file(s)");
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40 for (String inputFile : inputFiles) {
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41 try {
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42 WigFile wig = WigFile.autodetect(Paths.get(inputFile));
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43 wigs.add(wig);
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44 } catch (WigFileException e) {
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45 log.error("Error initializing Wig input file: " + inputFile);
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46 e.printStackTrace();
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47 throw new RuntimeException("Error initializing Wig input file: " + inputFile);
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48 }
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49 }
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50
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51 log.debug("Initializing output file");
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52 int count = 0, skipped = 0;
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53 try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
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54 writer.write("#Chr\tStart\tStop\tID\tValue\tStrand");
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55 for (String inputFile : inputFiles) {
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56 Path p = Paths.get(inputFile);
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57 writer.write("\t" + p.getFileName().toString());
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58 }
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59 writer.newLine();
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60
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61 log.debug("Iterating over all intervals and finding maxima");
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62 for (Interval interval : lociFile) {
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63 writer.write(interval.toBed());
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64 for (WigFile wig : wigs) {
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65 float maxValue = -Float.MAX_VALUE;
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66 int maxima = -1;
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67 try {
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68 Iterator<WigItem> results = wig.query(interval);
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69 while (results.hasNext()) {
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70 WigItem item = results.next();
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71 if (item.getWigValue() > maxValue) {
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72 maxValue = item.getWigValue();
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73 maxima = (item.getStartBase() + item.getEndBase()) / 2;
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74 }
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75 }
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76 writer.write("\t" + maxima);
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77 } catch (WigFileException e) {
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78 writer.write("\t" + Float.NaN);
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79 skipped++;
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80 }
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81 }
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82 writer.newLine();
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83 count++;
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84 }
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85 }
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86
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87 lociFile.close();
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88 for (WigFile wig : wigs) {
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89 wig.close();
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90 }
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91 log.info(count + " intervals processed");
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92 log.info(skipped + " interval skipped");
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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 FindAbsoluteMaxima().instanceMain(args);
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97 }
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98
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99 }
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