Is there a way to select a certain letter in Python?

Question

dna="AAGAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTCTTAGCGGGGCCACATCGGCCACCGCTGCCCTGCCCCTGGAGGGTGGCCCCACCGGCCGTTACAGCGAGCATAC"

So basically I was trying to select ONLY the letter "C"s in the dna variable, and simply replace it with the letter "G".

Is there a way/function I can have for this? Would be greatly appreciated if answered!

You'll need to do more than that to reverse complement your sequence ;) — Chris_Rands, Feb 04 '22 at 20:10
If you first replace all the `C` -> `G` how will you then replace all the `G` -> `C` ? Ex: `"CGCG".replace('C', 'G')` results in `"GGGG"`. — 001, Feb 04 '22 at 20:11

DarrylG · Accepted Answer · 2022-02-04T21:31:58.600

7

Use maketrans

Since you need: C <-> G and A <-> T

Meaning C -> G and G -> C, etc.

Example

dna = "CGATCCGG" # dna sequence

# Create translation table
x = "CGAT"       # original letters
y = "GCTA"       # letters to map too
mytable = str.maketrans(x, y)  # Create translation table
                               # dna.maketrans(x, y) also works

# Apply table to dna string
translated = dna.translate(mytable)

# Show Original vs. translated
print(f"Original:\t{dna}\nTranslate:\t{translated}")
# Output:
Original:   CGATCCGG
Translate:  GCTAGGCC

edited Feb 04 '22 at 21:31

answered Feb 04 '22 at 20:21

DarrylG

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@KellyBundy -- to create table you can either use an instance of a string (i.e. dna.maketrans...) or string class str (i.e. str.maketrans...). – DarrylG Feb 04 '22 at 20:43
@JohnnyMopp -- good point, expanded tabke with your suggestion. – DarrylG Feb 04 '22 at 20:49
Love you! Have a nice day! – KL777 Feb 05 '22 at 00:08

score 2 · Answer 2 · answered Feb 04 '22 at 20:08

2

You can use .replace():

dna=("AAGAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTCT"
"TAGCGGGGCCACATCGGCCACCGCTGCCCTGCCCCTGGAGGGTGGCCCCACCGGCCGTTACAGCGAGCATAC")

print(dna.replace("C", "G"))

answered Feb 04 '22 at 20:08

BrokenBenchmark

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Thank you very much sir! – KL777 Feb 04 '22 at 20:10

Asdoost · Answer 3 · 2022-02-04T23:42:42.490

2

If you want to replace Cs with Gs, use this:

dna.replace('C', 'G')

edited Feb 04 '22 at 23:42

answered Feb 04 '22 at 20:08

Asdoost

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Thank you very much sir! – KL777 Feb 04 '22 at 20:10

score -1 · Answer 4 · answered Feb 04 '22 at 20:15

for general replacement, you can use str.replace(target, replacement) but the issue in the context of the problem is that if you string replace all the C's with G's, you don't know what was originally a G to replace to a C to get the compliment.

It would be better to convert the strand into a list, then replace values one by 1 with case blocks or if/else blocks:

def dna_compliment(strand):
  listStrand = list(strand)
  for i in range(len(listStrand)):
     if listStrand[i] == 'C':
        listStrand[i] = 'G'
     elif ...
     ...
  return ''.join(listStrand)

Is there a way to select a certain letter in Python?

4 Answers4