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?

Perl will not *do it*, but you can *do it* in perl. But why? — ooga, Jun 18 '14 at 03:49
In the past, such low quality questions would receive only at most a few down-votes but this here shows some unhealthy religious-like zeal. Let's examine if that's the community we want to be. OP may have a perfectly reasonable explanation why Perl is preferred language here. Let's keep an open mind, shall we. — Roman Luštrik, Dec 04 '20 at 09:41

score 7 · Accepted Answer · answered Jun 18 '14 at 03:44

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.

1 Answers1