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