Mercurial > repos > timpalpant > java_genomics_toolkit

comparison java-genomics-toolkit/src/edu/unc/genomics/ngs/FindAbsoluteMaxima.java @ 0:1daf3026d231

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author timpalpant
date Mon, 13 Feb 2012 21:55:55 -0500
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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 }