Okay, having read a fair bit of 'Mastering Regular Expressions' today I'm going to attack this one.

Not going to fully comment the regexp, but essentially it does the following.. matches any number of ATCG's, then a single exception character which it stores in \1, then any number of ATCG's or \1s, then another single different exception character which it stores in \2, then any number of ATCG's, \1s, or \2s. This pattern is anchored to each end of the string too.

Sorry the regexp isn't nicely laid out, but it should work.

If this doesn't do quite what you want let me have some more test data and I'll fix it. Nice puzzle!

#!/usr/bin/perl -w

use strict;

my @tests = (
  'ATCG',
  'ATCGGTATATATRGTCGAYGCRGTCAGA',
  'ATCGGTATATATRGTCGAYGCNGTCAGA',
);

foreach (@tests) {
  if(/^[ATCG]*([RYMKSWHBVDN])?(?:[ATCG]|\1)*([RYMKSWHBVDN])?(?:[ATCG]|
+\1|\2)*$/i){
    print "$_ matches\n";
  } else {
    print "$_ does not match\n";
  }
}

[download]

Update: Slight change, original version demanded two exceptional codes. Oops.

Update 2: Yes, this is the same as Danger's code above. Ah well, two people coming up with the same solution at least inspires confidence.

In reply to Re: self limiting regex help by Molt
in thread self limiting regex help by spq

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