Mercurial > repos > timpalpant > java_genomics_toolkit
comparison java-genomics-toolkit/src/edu/unc/genomics/visualization/StripMatrix.java @ 0:1daf3026d231
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author | timpalpant |
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date | Mon, 13 Feb 2012 21:55:55 -0500 |
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-1:000000000000 | 0:1daf3026d231 |
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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 } |