So, the task is quite simple. I just need to replace all "T"s with "U"s in an input string of DNA. I have written the following code:
def transcribe_dna_to_rna(s):
base_change = {"t":"U", "T":"U"}
replace = "".join([base_change(n,n) for n in s])
return replace.upper()
and for some reason, I get the following error code:
'dict' object is not callable
Why is it that my dictionary is not callable? What should I change in my code? Thanks for any tips in advance!
To correctly convert DNA to RNA nucleotides in string s, use a combination of str.maketrans and str.translate, which replaces thymine to uracil while preserving the case. For example:
s = 'ACTGactgACTG'
s = s.translate(str.maketrans("tT", "uU"))
print(s)
# ACUGacugACUG
Note that in bioinformatics, case (lower or upper) is often important and should be preserved, so keeping both t -> u and T -> U is important. See, for example:
Uppercase vs lowercase letters in reference genome
SEE ALSO:
Character Translation using Python (like the tr command)
Note that there are specialized bioinformatics tools specifically for handling biological sequences.
For example, BioPython offers transcribe:
from Bio.Seq import Seq
my_seq = Seq('ACTGactgACTG')
my_seq = my_seq.transcribe()
print(my_seq)
# ACUGacugACUG
To install BioPython, use conda install biopython or conda create --name biopython biopython.
The syntax error tells you that base_change(n,n) looks like you are trying to use base_change as the name of a function, when in fact it is a dictionary.
I guess what you wanted to say was
def transcribe_dna_to_rna(s):
base_change = {"t":"U", "T":"U"}
replace = "".join([base_change.get(n, n) for n in s])
return replace.upper()
where the function is the .get(x, y) method of the dictionary, which returns the value for the key in x if it is present, and otherwise y (so in this case, return the original n if it's not in the dictionary).
But this is overcomplicating things; Python very easily lets you replace characters in strings.
def transcribe_dna_to_rna(s):
return s.upper().replace("T", "U")
(Stole the reordering to put the .upper() first from @norie's answer; thanks!)
If your real dictionary was much larger, your original attempt might make more sense, as long chains of .replace().replace().replace()... are unattractive and eventually inefficient when you have a lot of them.
In python 3, use str.translate:
dna = "ACTG"
rna = dna.translate(str.maketrans("T", "U")) # "ACUG"
Change s to upper and then do the replacement.
def transcribe_dna_to_rna(s):
return s.upper().replace("T", "U")
