How can I replace characters in a string in Python, but not using string methods?

Question

I just started learning Python, and I'm stuck in this problem: I have a DNA sequence, and I need to return its complementary sequence. For example, if I have ATTGCA, it should return TAACGT. This is, replace A by T, T by A, C by G and G by C. It's an exercise, and I'm not supposed to use string methods. Everything I tried until now, return me 'T' as answer. Seems it only recognize the first letter, then stops. How can I do it?

I tried:

>>> def get_complementary_sequence(dna):
    for char in dna:
        if char == 'A':
            return 'T'
        elif char == 'T':
            return 'A'
        elif char == 'C':
            return 'G'
        elif char == 'G':
            return 'C'


>>> get_complementary_sequence('ATTGCA')
'T'

And also tried:

def get_complementary_sequence(dna):
    sequence = ""
    for nucleotide in dna:
        if nucleotide == 'A':
            return sequence + 'T'
        elif nucleotide == 'T':
            return sequence + 'A'
        elif nucleotide == 'C':
            return sequence + 'G'
        elif nucleotide == 'G':
            return sequence + 'C'
        return sequence


>>> get_complementary_sequence('ATTGCA')
'T'

Everything I tried until now -> then show us what you tried? — Rohit Jain
– Rohit Jain, Commented Oct 18, 2012 at 20:09
>>> def get_complementary_sequence(dna): for char in dna: if char == 'A': return 'T' elif char == 'T': return 'A' elif char == 'C': return 'G' elif char == 'G': return 'C' >>> get_complementary_sequence('ATTGCA') 'T' >>> — Luiz Maurício R. Menezes
– Luiz Maurício R. Menezes, Commented Oct 18, 2012 at 20:56

Ashwini Chaudhary · Accepted Answer · 2012-10-18 20:23:06Z

5

try a dictionary, that way you'll also don't need the if's and elif's:

In [45]: dic={'A':'T','T':'A','C':'G','G':'C'}

In [46]: strs="ATTGCA"

In [47]: ''.join(dic[x] for x in strs)
Out[47]: 'TAACGT'

or using map():

In [52]: ''.join(map(dic.get,strs))
Out[52]: 'TAACGT'

edited Oct 18, 2012 at 20:23

answered Oct 18, 2012 at 20:13

Ashwini Chaudhary

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6 Comments

Laurence Gonsalves Over a year ago

join is a "string method", so I wonder if this meets the requirements. Though I suppose one could argue that even + is a string method (__add__).

Ashwini Chaudhary Over a year ago

@LaurenceGonsalves IMHO the string method he's concerned with is replace().

Laurence Gonsalves Over a year ago

Maybe. He said "I'm not supposed to use string methods" not "I'm not supposed to use replace()".

Tim Pietzcker Over a year ago

@AshwiniChaudhary: I would have been more concerned about his using "ATAGGTCTCTTA".translate({65: 84, 67: 71, 84: 65, 71: 67}). replace() would have been difficult to use because of the symmetric replacements...

Ashwini Chaudhary Over a year ago

@TimPietzcker I never knew about this method ,thanks for that. But this only works in py3k I guess?

|

Mark Ransom · Accepted Answer · 2012-10-18 20:10:34Z

3

A string is also a sequence of characters, so you can iterate through it:

for char in sequence:

answered Oct 18, 2012 at 20:10

Mark Ransom

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Comments

Alexander Stefanov · Accepted Answer · 2012-10-18 20:21:19Z

2

Here is an equivalent of Ashwini Chaudhary's elegant solution which maybe more comprehensible for beginners:

complements = {'A': 'T',
               'T': 'A',
               'C': 'G',
               'G': 'C'}
dna_sequence = 'ATTGCA'
new_sequence = []
for char in dna_sequence:
    new_sequence.append(complements[char])
# new_sequence is now ['T', 'A', 'A', 'C', 'G', 'T']
result = ''.join(new_sequence) # result in 'TAACGT'

answered Oct 18, 2012 at 20:21

Alexander Stefanov

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Tim Pietzcker · Accepted Answer · 2012-10-18 20:38:18Z

2

Another way using dictionaries, entirely without string methods :)

trans = {'A':'T','T':'A','C':'G','G':'C'}
with open("temp.txt", "w") as outfile:
    for character in mystring:
        outfile.write(trans[character])
with open("temp.txt") as infile:
    result = infile.read()

answered Oct 18, 2012 at 20:38

Tim Pietzcker

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2 Comments

Ashwini Chaudhary Over a year ago

+1 why doesn't this came to my mind :), but you can reduce your solution to this

smci Over a year ago

Neat. You might like to use Python tempfile

Michael Nico · Accepted Answer · 2013-09-12 08:10:37Z

1

This solution is easy to understand. Hope it helps.

def get_complement(nucleotide):
    """ (str) ->str
    """

    sequence = ""
    for char in nucleotide:
        if char == "A":
            sequence = sequence + "T"
        if char == "T":
            sequence = sequence + "A"
        if char == "G":
            sequence = sequence + "C"
        if char == "C":
            sequence = sequence + "G"

    return sequence

edited Sep 12, 2013 at 8:10

answered Sep 12, 2013 at 5:52

Michael Nico

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