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1 package edu.unc.genomics.converters;
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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 import java.util.regex.Matcher;
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10 import java.util.regex.Pattern;
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11
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12 import org.apache.log4j.Logger;
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13
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14 import com.beust.jcommander.Parameter;
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15
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16 import edu.unc.genomics.CommandLineTool;
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17 import edu.unc.genomics.ReadablePathValidator;
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18 import edu.unc.utils.RomanNumeral;
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19
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20 public class RomanNumeralize extends CommandLineTool {
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21
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22 private static final Logger log = Logger.getLogger(RomanNumeralize.class);
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23
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24 @Parameter(names = {"-i", "--input"}, description = "Input file", required = true, validateWith = ReadablePathValidator.class)
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25 public Path inputFile;
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26 @Parameter(names = {"-o", "--output"}, description = "Output file", required = true)
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27 public Path outputFile;
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28
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29 /**
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30 * Pattern for finding "chr12" tokens (will find "chr1" through "chr99")
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31 */
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32 Pattern p = Pattern.compile("/chr[\\d]{1,2}/i");
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33
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34 @Override
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35 public void run() throws IOException {
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36 try (BufferedReader reader = Files.newBufferedReader(inputFile, Charset.defaultCharset());
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37 BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
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38 log.debug("Copying input to output and replacing with Roman Numerals");
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39 String line;
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40 while ((line = reader.readLine()) != null) {
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41 Matcher m = p.matcher(line);
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42 StringBuffer converted = new StringBuffer(line.length());
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43 while (m.find()) {
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44 String chrNum = line.substring(m.start()+3, m.end());
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45 int arabic = Integer.parseInt(chrNum);
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46 String roman = RomanNumeral.int2roman(arabic);
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47 m.appendReplacement(converted, "chr"+roman);
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48 }
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49 m.appendTail(converted);
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50
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51 writer.write(converted.toString());
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52 writer.newLine();
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53 }
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54 }
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55 }
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56
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57 public static void main(String[] args) {
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58 new RomanNumeralize().instanceMain(args);
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59 }
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60
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61 }
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