What is the best, python or bash for generating strings from combinations of letters?

Question

Hi,

I need to generate the strings STA and STB.

STA and STB are strings of length 10, and each one can contain only the characters A,T,G or C.

I have to generate all possible combinations of STA, and depending on STA, I generate STB.

The ways is that the character A is always associated with T and viceversa and G with C and viceversa.

so it is possible combinations like:

STA: ATGC...
STB: TACG...

or

STA: GTTA...
STB: CAAT...

and so on.

I wonder what would be the best way of doing this using bash or python

Thanks

Answer 1

I'd say Python.

Have a look here for string permutations: Permutations using a Combinations Generator (Python). Another thing to look at is itertools in Python 2.6+ - Generating all permutations of a list in python. I do note however that your requirements are more in depth, however you will probably find it easier to add in the necessary constraints in Python rather than Bash.

Simple, clean and easy.

Now, I'm not expert on Bash, but looking at it, you would have to have multiple lines that repeat pretty much the same text over and over depending on your combinations. It would be great to use simple combinations, but not linked combinations.

Answer 2

While I don't know bash and don't see how permutations would solve your problem, it seems that itertools.product is a fairly straightforward way to do this:

>>> s = 'atgc'
>>> d = dict(zip(s, 'tacg'))
>>> import itertools
>>> for i in itertools.product(s, repeat=10):
    sta = ''.join(i)
    stb = ''.join(d[x] for x in i)

while proposed method is valid in terms of obtaining all possible permutations with replacement of the 'atgc' string, i.e., finding sta string, finding stb would be more efficient not through the dictionary look-up, but rather the translation mechanism:

>>> trans = str.maketrans(s, 'tacg')
>>> for i in itertools.product(s, repeat=10):
    sta = ''.join(i)
    stb = sta.translate(trans)

Thanks to Dave, for highlighting more efficient solution.

Answer 3

Unrelated to your actual question but related to what you're (apparently) doing, have you checked out BioPython?

Answer 4

Here you go:

>>> from itertools import product
>>> seq = ("AGCT",) * 10
>>> STA = [''.join(a) for a in product(*seq)]
>>> STB = list(reversed(STA))

Incidentally, len(STA) is 2²⁰.

itertools.product is available in Python 2.6.

See @hop's answer here for an implementation of product in Python 2.5

Answer 5

Others have said how to generate STA.

The most efficient way to convert a string STA into the equivalent string STB is to use the string translate & maketrans functions.

>>> import string
>>> s = "AGTC" * 100
>>> trans = string.maketrans("ATGC", "TACG")
>>> s.translate(trans)
'TCAG...TCAG'

On my system this is ~100 times faster than doing a dictionary lookup on each character as suggested by SilentGhost.

Answer 6

bash baby :)

STA=$(echo {A,C,T,G}{A,C,T,G}{A,C,T,G}{A,C,T,G}{A,C,T,G}{A,C,T,G}{A,C,T,G}{A,C,T,G}{A,C,T,G}{A,C,T,G})
STB=$(echo $STA | tr ATCG TAGC)

echo $STA
echo $STB