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Asked: 2026-06-11T17:19:04+00:00

I need to parse Newick format that is useful for trees. It looks like

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I need to parse Newick format that is useful for trees. It looks like series of brackets, commas and letters denoted nodes:

(A,B,(C,D)E)F

or, for another example:

(,(((,(,)),),))

(,) element means nodes with same parent. For my purpose (to measure a path length between two leafs) I need consequentially to look for such nested elements.

So, my question is how to match different symbols same number of times?

For example, I want to match AB pattern in string: 

CCCAAABBACCCABCCAAABBBBBBACCCCCABBBABBCCAABB

Regex should return: ['AABB','AB','AAABBB','AB','AB','AABB']

Every time the number of repetition is different. So A{n}B{n} doesn’t work.

Thanks.

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1 Answer

  1. Editorial Team

    Your problem is classic example what regular expressions can’t do.

    http://en.wikipedia.org/wiki/Pumping_lemma_for_regular_languages in section “Use of lemma” there is prove that language “a^nb^n” is not regular (so it can’t be recognized by regular expressions).

    Using regular expression you can only create regular expressions for a given maximum n. But expression for large n can take long to evaluate.

    PS. Your problem can be solved using Formal grammars (http://en.wikipedia.org/wiki/Formal_grammar) or Counter automaton (http://en.wikipedia.org/wiki/Counter_automaton).

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