CODEWITHSUNDEEP
python
user4512750
user4512750

Reputation:

String converter program not working

I am trying to make a basic program which translates a string ATGTACATGGGCATAGCCATATA to its RNA sequence, which is UACAUGUACCCGUAUCGGUAUAU.

But instead the output is: CCCCCUUUUUUUUUUUUUUUUUUUUUUU

But it's not quite working. I think the problem is it goes through the entire string with each letter individually.

I am very new to bioinformatics programming so any suggestions would be welcomed.

DNA = "ATGTACATGGGCATAGCCATATA"
dna_length = len(DNA)

print("DNA: " + DNA)
print()
print("Length of DNA in base pairs: "+ str(dna_length))

RNA = []
for char in DNA:
    if char == "G":
        RNA.append("C")
for line in DNA:
    if char == "C":
        RNA.append("G")
for line in DNA:
    if char == "A":
        RNA.append("U")
for line in DNA:
    if char == "T":
        RNA.append("A")

print("".join(RNA))

Upvotes: 1

Views: 63

Answers (4)

Ashwini Chaudhary
Ashwini Chaudhary

Reputation: 250921

The problem is that you're looping over the same list four times and also modifying the changes that were made in the previous loops. So, use a single loop with multiple if-else conditions:

RNA = []
for char in DNA:
    if char == "G":
        RNA.append("C")
    elif char == "C":
        RNA.append("G")
    elif char == "A":
        RNA.append("U")
    elif char == "T":
        RNA.append("A")

print("".join(RNA))

Best solution will be to use str.translate:

>>> from string import maketrans
>>> s = "ATGTACATGGGCATAGCCATATA"
>>> tab = maketrans('GCAT', 'CGUA')
>>> s.translate(tab)
'UACAUGUACCCGUAUCGGUAUAU'

In Python 3 we can do it without any imports:

>>> s = "ATGTACATGGGCATAGCCATATA"
>>> s.translate({ord(k): v for k, v in zip('GCAT', 'CGUA')})
'UACAUGUACCCGUAUCGGUAUAU'

Upvotes: 3

Antti Haapala -- Слава Україні
Antti Haapala -- Слава Україні

Reputation: 133899

There is str.maketrans which makes a translation table from 1 set of characters to another, and str.translate which applies such mapping to a string; this should be the fastest way to do this, thus

>>> DNA_2_RNA = str.maketrans('CGAT', 'GCUA')
>>> DNA = 'ATGTACATGGGCATAGCCATATA'
>>> RNA = DNA.translate(DNA_2_RNA)
>>> RNA
'UACAUGUACCCGUAUCGGUAUAU'

Upvotes: 2

Abhinav Ramakrishnan
Abhinav Ramakrishnan

Reputation: 1090

Corrected Code:

DNA = "ATGTACATGGGCATAGCCATATA"
dna_length = len(DNA)

print("DNA: " + DNA)
print()
print("Length of DNA in base pairs: "+ str(dna_length))

RNA = []
for char in DNA:
    if char == "G":
        RNA.append("C")
    elif char == "C":
        RNA.append("G")
    elif char == "A":
        RNA.append("U")
    elif char == "T":
        RNA.append("A")

print("".join(RNA))

Result:

DNA: ATGTACATGGGCATAGCCATATA
()
Length of DNA in base pairs: 23
UACAUGUACCCGUAUCGGUAUAU

Upvotes: 0

Cory Kramer
Cory Kramer

Reputation: 117856

I would use a dict to perform your substitutions, then use a generator expression within join to perform your translation.

>>> RNA = {'G':'C', 'C':'G', 'A':'U', 'T':'A'}
>>> DNA = 'ATGTACATGGGCATAGCCATATA'
>>> translated = ''.join(RNA[i] for i in DNA)
>>> translated
'UACAUGUACCCGUAUCGGUAUAU'

Upvotes: 3

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