Complement a DNA sequence

Question

Suppose I have a DNA sequence. I want to get the complement of it. I used the following code but I am not getting it. What am I doing wrong ?

s=readline()
AT         


        

Answer 1

Use chartr which is built for this purpose:

> s
[1] "ATCTCGGCGCGCATCGCGTACGCTACTAGC"
> chartr("ATGC","TACG",s)
[1] "TAGAGCCGCGCGTAGCGCATGCGATGATCG"

Just give it two equal-length character strings and your string. Also vectorised over the argument for translation:

> chartr("ATGC","TACG",c("AAAACG","TTTTT"))
[1] "TTTTGC" "AAAAA" 

Note I'm doing the replacement on the string representation of the DNA rather than the vector. To convert the vector I'd create a lookup-map as a named vector and index that:

> p
 [1] "A" "T" "C" "T" "C" "G" "G" "C" "G" "C" "G" "C" "A" "T" "C" "G" "C" "G" "T"
[20] "A" "C" "G" "C" "T" "A" "C" "T" "A" "G" "C"
> map=c("A"="T", "T"="A","G"="C","C"="G")
> unname(map[p])
 [1] "T" "A" "G" "A" "G" "C" "C" "G" "C" "G" "C" "G" "T" "A" "G" "C" "G" "C" "A"
[20] "T" "G" "C" "G" "A" "T" "G" "A" "T" "C" "G"