Why is re.findall not being specific in finding triplet items in string. Python

Question

So I have four lines of code

seq= \'ATGGAAGTTGGATGAAAGTGGAGGTAAAGAGAAGACGTTTGA\'



OR_0 = re.findall(r\'ATG(?:...){9,}?(?:TAA|TAG|TGA)\',seq)  

Answer 1

If you want your regex to stop matching at the first TAA|TAG|TGA, but still only succeed if there are at least nine three letter chunks, the following may help:

>>> import re
>>> regexp = r'ATG(?:(?!TAA|TAG|TGA)...){9,}?(?:TAA|TAG|TGA)'
>>> re.findall(regexp, 'ATGAAAAAAAAAAAAAAAAAAAAAAAAAAATAG')
['ATGAAAAAAAAAAAAAAAAAAAAAAAAAAATAG']
>>> re.findall(regexp, 'ATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAG')
['ATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAG']
>>> re.findall(regexp, 'ATGAAATAGAAAAAAAAAAAAAAAAAAAAATAG')
[]

This uses a negative lookahead (?!TAA|TAG|TGA) to ensure that a three character chunk is not a TAA|TAG|TGA before it matches the three character chunk.

Note though that a TAA|TAG|TGA that does not fall on a three character boundary will still successfully match:

>>> re.findall(regexp, 'ATGAAAATAGAAAAAAAAAAAAAAAAAAAATAG')
['ATGAAAATAGAAAAAAAAAAAAAAAAAAAATAG']