Question

I’m a python newbie but have programmed a while in other languages. I have a long string of DNA (lower case) and AA sequences (upper case). Further at the start of the file I have a protein name all in upper case. Thus my file looks like this.

PROTEINNAMEatcgatcg… JFENVKDFDFLK

I need to find the first non-uppercase letter in the string so I can then cut out the protein name. Thus, what I would want from the above is:

atcgatcg… JFENVKDFDFLK

I can do this with a loop but that seems like overkill and inefficient. Is there a simply python way to do it?

I can get all the uppercase letters using re.findall(“[A-Z]”,mystring) but then I would need to do a comparison to see where the result differs from the original string.

Thanks!

Answer 1

You are almost there with your regex… but there are other methods besides findall:

http://docs.python.org/library/re.html#re.sub

>>> import re
>>> protein_regex = re.compile('^[A-Z]+')
>>> dna = 'PROTEINNAMEatcgatcg... JFENVKDFDFLK'
>>> protein_regex.sub('', dna)
'atcgatcg... JFENVKDFDFLK'

Not sure about performance, but you could also do

>>> import string
>>> dna.lstrip(string.uppercase)
'atcgatcg... JFENVKDFDFLK'

And there you have it:

python -m timeit -n 10000 -s 'import re' -s 'protein_regex = re.compile("^[A-Z]+")' -s 'dna = "PROTEINNAMEatcgatcg... JFENVKDFDFLK"' 'protein_regex.sub("", dna)'
10000 loops, best of 3: 1.36 usec per loop

python -m timeit -n 10000 -s 'import string' -s 'dna = "PROTEINNAMEatcgatcg... JFENVKDFDFLK"' 'dna.lstrip(string.uppercase)'
10000 loops, best of 3: 0.444 usec per loop

Second one looks to be ~3 times faster.