Substituting nucleotides in Python

Question

The problem is to first reverse the string. Then swap "T" for "A", and vice versa, and "G" for "C", and vice versa. I have no problem reversing the string. The problem is replacing T with A and vice versa and also with G and C and vice versa since the replace methods cancel each other out.

Here is my code:

s = str(raw_input("Enter a string: ")) 
reversed = s[::-1] 

if "T" and "A" and "G" and "C" in reversed: 
    reversed.replace("A", "T") 
    reversed.replace("T", "A")
    reversed.replace("C", "G")
    reversed.replace("G", "C") 

print reversed 

Any help or suggestions would be greatly appreciated.

Answer 1

Another, concise way:

trans_table_AT_CG = str.maketrans({
        'T': 'A',
        'A': 'T',
        'C': 'G',
        'G': 'C'
})
def gene_swap_str(s):
    return s[::-1].translate(trans_table_AT_CG)

So now you can write:

s = input("Enter a string: ").upper()    # Py2: raw_input
print(gene_swap_str(s))

This is a Python 3 answer: in Python 2, str.maketrans can't take a single dict argument, but only two equal-length strings from, to (still supported in Py3). In Py2, you'd use

trans_table_AT_CG = str.maketrans('ATCG', 
                                  'TAGC')    # Py2 and Py3

instead -- this works in Py3 as well, but I find the two parallel strings less clear than the dict. Of course, in Py2, use raw_input not input; in either case, you don't need to wrap the result in str(), as both return strings.

Answer 2

This is a case where you might consider using a function because it's more portable and reusable in later parts of code. Here is a simple solution to your problem:

def geneSwap(c):
    return {
        'A': 'T',
        'T': 'A',
        'C': 'G',
        'G': 'C',
    }[c]

s = str(raw_input("Enter a string: ")) 
reversed = s[::-1] 

[geneSwap(c) for c in reversed]

print reversed 

However, Python's list processing capabilities allow for much more condensed coding. This uses the geneSwap() function and reverses the sequence all in one line (shiny!):

def geneSwap(c):
    return {
        'A': 'T',
        'T': 'A',
        'C': 'G',
        'G': 'C',
    }[c]

s = str(raw_input("Enter a string: ")) 

print ''.join( [geneSwap(c) for c in s[::-1]] )

** Thanks @BrianO for the correction on the print line.

For those unfamiliar with the code in the print statement in the second code block, the list operation can be broken down into steps from right to left:

1. s is a string which can be treated as a list of characters. So the list operation [::-1] returns an iterator which increments through the list by increments of -1 from (but not including) the beginning to the beginning (or, from the end to the beginning in reverse order)
2. [geneSwap(c) for c in s[::-1]] (or you could replace s[::-1] for any list) executes the function on every element c in the list and returns it as a list.
3. The last part is a ''.join(). You'll notice that step 2 results in a list - not a string. Since the OP wants a string, the last step is to compose a string from the list characters. This is done using the join() string function which joins elements of the passed list using the string the join() is used on. In this case, the OP wants the characters strung together with nothing separating them. So an empty string is used. If the OP wanted spaces or dashes (-) they would use ' '.join() or '-'.join() respectively.

Inspired by Call int() function on every list element?

Answer 3

You can iterate over the string and replace chars as you go.
BTW, this check is not going to work: if "T" and "A" and "G" and "C" in reversed. You can use all() instead.

if all(char in reversed for char in "TAGC"):
    cmap = dict(zip("ATCG", "TAGC"))
    reversed = "".join([cmap[c] for c in reversed])

print(reversed)

Answer 4

simply iterating over the characters will be cheap timewise:

buffer = ""
for c in string:
    if c == "T":
        buffer += "A"
    elif c == "A":
    ... # etc.
# do as you will with buffer

Answer 5

I think it is more simple in Python 3. e.g.:

def nucleo(dna):
    return dna.translate(str.maketrans("ATCG","TAGC"))
print(nucleo("ACTG"))