frequency of letters at position in string

Question

I want to count the frequency of 4 letters at every position across strings. The letters are A, T, G, C

TGAGGTAGTAGTTTGTGCTGTTAT
TAGTAGTTTGTGCTGTTA
TGAGGTAGTAGTTTGTAC
TGAGAACTGAATTCCATAGG

desired output:

  Pos1  Pos2  Pos3  and so on. 
A 0     1
T 4     0
C 0     0
G 0     3

So far I have used an R package called Biostrings, which works, but I wonder if perl would do this?

Answer 1

For the record, for

x = "TGAGGTAGTAGTTTGTGCTGTTAT
TAGTAGTTTGTGCTGTTA
TGAGGTAGTAGTTTGTAC
TGAGAACTGAATTCCATAGG"

a Biostrings solution is

library(Biostrings)
consensusMatrix(DNAStringSet(strsplit(x, "\n")[[1]]))

which will be fast for millions of sequences.