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a guest Oct 13th, 2019 74 Never
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  1. import java.io.*;
  2. import java.util.*;
  3. import java.util.regex.*;
  4.  
  5. public class CountCosmicOccurrence {
  6.     public static void main(String[] args) throws IOException {
  7.         // input format:
  8.         // annovar cosmic format
  9.         // ID=COSM13127;OCCURENCE=12(stomach),2(endometrium),3(soft_tissue),158(large_intestine),2(pancreas),6(small_intestine)
  10.         // the blank line will output 0
  11.         // like "lofreq_CTCTUTOvlp_cosmic70"
  12.         BufferedReader br = new BufferedReader(new FileReader(args[0]));
  13.         String line = null;
  14.         Pattern p = Pattern.compile("(\\d+)\\(");
  15.         Matcher m = null;
  16.         while((line = br.readLine()) != null) {
  17.             if(line.equals("")) {
  18.                 System.out.println(0);
  19.             } else {
  20.                 m = p.matcher(line);
  21.                 int count = 0;
  22.                 while(m.find()) {
  23.                     count += Integer.parseInt(m.group(1));
  24.                 }
  25.                 System.out.println(count);
  26.             }
  27.         }
  28.         br.close();
  29.     }
  30. }
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