How can I extract multine data using a regex? ... driving me nuts!!

Question

Hi everyone,
I have a file which I'm interested in extracting information from. Here is a snippet:
CGCNNNNGTAGTC
TAGTCNN
... my goal is to create a regex which extracts out everything beyond the N (on the first line), along with anything on the next line which is not N.
As a result, my desired outcome is "GTAGTCTAGTC"
What I've worked on sofar (for my regex) is:
Pattern p = Pattern.compile("(N[ATGC].*)\\r\\n[ATGC].*N", Pattern.MULTILINE);I've worked on it for sometime now, and am very interested in advice as-to how I can extract my desired information.
Thanks once again,
p.
Edited by: phosse1 on Apr 9, 2009 8:37 PM
Edited by: phosse1 on Apr 9, 2009 8:38 PM

Answer 1

Till one of the regex gurus comes around to shorten the regex by 50% and increase the readability and efficiency by 1000% ;-)import java.util.regex.Matcher;
import java.util.regex.Pattern;
public class CrossLineMatcher {
   public static void main(String[] args) {
      String[] inputs = {
         "CGCNNNNGTAGTC\n" +
         "TAGTCNN",
         "CGCNNNNGTAGTC\r\n" +
         "TAGTCNN",
         "CGCNNNNGTAGTC\r" +
         "TAGTCNN",
      String regex = "(?m)(?<=N)([^N]+)(?:$[\\r\\n]+^)([^N]+)(?=N)";
      Pattern pattern = Pattern.compile(regex, Pattern.MULTILINE);
      for (String input : inputs) {
         Matcher matcher = pattern.matcher(input);
         while (matcher.find()) {
            System.out.println(matcher.group(1)+matcher.group(2));
      System.out.println("=======================");
      regex = "(?m).*?N([^N]+)(?:$[\\r\\n]+^)([^N]+)N.*?";
      for (String input : inputs) {
         System.out.println(input.replaceAll(regex, "$1$2"));
everything beyond the N (on the first line), along with anything on the next line which is not NYou want to express a match for "anything that is not N", use [^N]
[ATGC] means "anything that is A, T, G or C"
db