Mercurial > repos > timpalpant > java_genomics_toolkit

comparison src/edu/unc/genomics/visualization/StripMatrix.java @ 2:e16016635b2a

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author timpalpant
date Mon, 13 Feb 2012 22:12:06 -0500
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1:a54db233ee3d 2:e16016635b2a
1 package edu.unc.genomics.visualization;
2
3 import java.io.BufferedReader;
4 import java.io.BufferedWriter;
5 import java.io.IOException;
6 import java.nio.charset.Charset;
7 import java.nio.file.Files;
8 import java.nio.file.Path;
9
10 import org.apache.log4j.Logger;
11
12 import com.beust.jcommander.Parameter;
13
14 import edu.unc.genomics.CommandLineTool;
15 import edu.unc.genomics.ReadablePathValidator;
16
17 public class StripMatrix extends CommandLineTool {
18
19 private static final Logger log = Logger.getLogger(StripMatrix.class);
20
21 @Parameter(names = {"-i", "--input"}, description = "Input file (matrix2png format)", required = true, validateWith = ReadablePathValidator.class)
22 public Path inputFile;
23 @Parameter(names = {"-o", "--output"}, description = "Output file (tabular)", required = true)
24 public Path outputFile;
25
26 public void run() throws IOException {
27 try (BufferedReader reader = Files.newBufferedReader(inputFile, Charset.defaultCharset())) {
28 try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
29 String line = reader.readLine();
30 // Always copy the first (header) line
31 writer.write(line);
32 writer.newLine();
33 while ((line = reader.readLine()) != null) {
34 String[] row = line.split("\t");
35 for (int i = 1; i < row.length; i++) {
36 String cell = row[i];
37 if (cell.equalsIgnoreCase("-")) {
38 writer.write("NaN");
39 } else {
40 writer.write(cell);
41 }
42
43 if (i > 1) {
44 writer.write("\t");
45 }
46 }
47 writer.newLine();
48 }
49 }
50 }
51 }
52
53 public static void main(String[] args) {
54 new StripMatrix().instanceMain(args);
55 }
56 }