Mercurial > repos > timpalpant > java_genomics_toolkit

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