|
0
|
1 package edu.unc.genomics.ngs;
|
|
|
2
|
|
|
3 import java.io.BufferedWriter;
|
|
|
4 import java.io.IOException;
|
|
|
5 import java.nio.charset.Charset;
|
|
|
6 import java.nio.file.Files;
|
|
|
7 import java.nio.file.Path;
|
|
|
8 import java.nio.file.Paths;
|
|
|
9 import java.util.ArrayList;
|
|
|
10 import java.util.Iterator;
|
|
|
11 import java.util.List;
|
|
|
12
|
|
|
13 import org.apache.log4j.Logger;
|
|
|
14 import org.broad.igv.bbfile.WigItem;
|
|
|
15
|
|
|
16 import com.beust.jcommander.Parameter;
|
|
|
17
|
|
|
18 import edu.unc.genomics.CommandLineTool;
|
|
|
19 import edu.unc.genomics.Interval;
|
|
|
20 import edu.unc.genomics.io.IntervalFile;
|
|
|
21 import edu.unc.genomics.io.WigFile;
|
|
|
22 import edu.unc.genomics.io.WigFileException;
|
|
|
23
|
|
|
24 public class FindAbsoluteMaxima extends CommandLineTool {
|
|
|
25
|
|
|
26 private static final Logger log = Logger.getLogger(FindAbsoluteMaxima.class);
|
|
|
27
|
|
|
28 @Parameter(description = "Input files", required = true)
|
|
|
29 public List<String> inputFiles = new ArrayList<String>();
|
|
|
30 @Parameter(names = {"-l", "--loci"}, description = "Loci file (Bed)", required = true)
|
|
|
31 public IntervalFile<? extends Interval> lociFile;
|
|
|
32 @Parameter(names = {"-o", "--output"}, description = "Output file", required = true)
|
|
|
33 public Path outputFile;
|
|
|
34
|
|
|
35 private List<WigFile> wigs = new ArrayList<>();
|
|
|
36
|
|
|
37 @Override
|
|
|
38 public void run() throws IOException {
|
|
|
39 log.debug("Initializing input Wig file(s)");
|
|
|
40 for (String inputFile : inputFiles) {
|
|
|
41 try {
|
|
|
42 WigFile wig = WigFile.autodetect(Paths.get(inputFile));
|
|
|
43 wigs.add(wig);
|
|
|
44 } catch (WigFileException e) {
|
|
|
45 log.error("Error initializing Wig input file: " + inputFile);
|
|
|
46 e.printStackTrace();
|
|
|
47 throw new RuntimeException("Error initializing Wig input file: " + inputFile);
|
|
|
48 }
|
|
|
49 }
|
|
|
50
|
|
|
51 log.debug("Initializing output file");
|
|
|
52 int count = 0, skipped = 0;
|
|
|
53 try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
|
|
|
54 writer.write("#Chr\tStart\tStop\tID\tValue\tStrand");
|
|
|
55 for (String inputFile : inputFiles) {
|
|
|
56 Path p = Paths.get(inputFile);
|
|
|
57 writer.write("\t" + p.getFileName().toString());
|
|
|
58 }
|
|
|
59 writer.newLine();
|
|
|
60
|
|
|
61 log.debug("Iterating over all intervals and finding maxima");
|
|
|
62 for (Interval interval : lociFile) {
|
|
|
63 writer.write(interval.toBed());
|
|
|
64 for (WigFile wig : wigs) {
|
|
|
65 float maxValue = -Float.MAX_VALUE;
|
|
|
66 int maxima = -1;
|
|
|
67 try {
|
|
|
68 Iterator<WigItem> results = wig.query(interval);
|
|
|
69 while (results.hasNext()) {
|
|
|
70 WigItem item = results.next();
|
|
|
71 if (item.getWigValue() > maxValue) {
|
|
|
72 maxValue = item.getWigValue();
|
|
|
73 maxima = (item.getStartBase() + item.getEndBase()) / 2;
|
|
|
74 }
|
|
|
75 }
|
|
|
76 writer.write("\t" + maxima);
|
|
|
77 } catch (WigFileException e) {
|
|
|
78 writer.write("\t" + Float.NaN);
|
|
|
79 skipped++;
|
|
|
80 }
|
|
|
81 }
|
|
|
82 writer.newLine();
|
|
|
83 count++;
|
|
|
84 }
|
|
|
85 }
|
|
|
86
|
|
|
87 lociFile.close();
|
|
|
88 for (WigFile wig : wigs) {
|
|
|
89 wig.close();
|
|
|
90 }
|
|
|
91 log.info(count + " intervals processed");
|
|
|
92 log.info(skipped + " interval skipped");
|
|
|
93 }
|
|
|
94
|
|
|
95 public static void main(String[] args) {
|
|
|
96 new FindAbsoluteMaxima().instanceMain(args);
|
|
|
97 }
|
|
|
98
|
|
|
99 }
|
