Substrings of whole string in R

Question

This type of question is already asked many times, however I could not get the answer according to my needs.

I know some way of splitting strings in R. If I have a string x <- "AGCAGT", and want to split the string into characters of three. I would do this by

substring(x, seq(1, nchar(x)-1, 3), seq(3, nchar(x), 3))

and string of two character much faster by

split <- strsplit(x, "")[[1]]
substrg <- paste0(split[c(TRUE, FALSE)], split[c(FALSE, TRUE)])

As a new user of R, I feel difficulty to split string according to my requirements. If x <- "AGCTG" and if I use substring(x, seq(1, nchar(x)-1, 3), seq(3, nchar(x), 3)), I do not get the last two character substring. I get

"AGC" ""

However I am interested to get something like

"AGC" "TG"

or if I have x <- "AGCT" and splitting 3 characters at a time, I would like to get some thing like

"AGC" "T"`

I short, how to split a string into substrings of desired length (2,3,4,5...n), and also retaining those remaining characters less than the desired length.

See the output of `seq(3, nchar(x), 3)`, which is the end of the substring and you'll get what the problem is. — nicola, Feb 25 '16 at 11:31
It appears that there [there is an answer](http://stackoverflow.com/a/23262521/1655567) concerned with precisely the same problem. — Konrad, Feb 25 '16 at 11:42
The marked duplicate does not solve my problem. The answer by `zx8754`, however, later deleted seems to solve my problem — Khawaja Owaise Hussain, Feb 25 '16 at 11:52
@zx8754 Please consider to undelete the post. As per the OP's concerns, I am reopening the post. — akrun, Feb 25 '16 at 14:29
@RichardScriven Please check my desired output above. Consider string `AGCGGCCAGCT` and three character split. — Khawaja Owaise Hussain, Feb 25 '16 at 15:03
@akrun Thanks for reopening the post. Indeed not a duplicate, some rushed to mark it as duplicate. The solution @zx8754 works perfect. `x <- "AGCGGCCAGCTGCCTGAA" mylen <- 5 ss <- strsplit(x, "")[[1]] v1 <- sapply(split(ss, ceiling(seq_along(ss)/mylen)), paste, collapse = "")` — Khawaja Owaise Hussain, Feb 25 '16 at 15:18
This is pretty confusing to follow as all solutions are comments. — cory, Feb 25 '16 at 16:01

cdeterman · Accepted Answer · 2016-02-25T16:18:36.867

1

Here is one possible solution in a few simple steps.

x <- "AGCGGCCAGCTGCCTGAA"

# desired length
mylen = 5

# start indices
start <- seq(1, nchar(x), mylen)

# end indicies
end <- pmin(start + mylen - 1, nchar(x))

substring(x, start, end)
[1] "AGCGG" "CCAGC" "TGCCT" "GAA"

edited Feb 25 '16 at 16:18

answered Feb 25 '16 at 16:09

cdeterman

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score 1 · Answer 2 · answered Feb 25 '16 at 16:25

Answer by zx8754. But unfortunately he deleted the answer after some marked the question as duplicate. If he would like to post this as an answer, I'l delete my post.

x <- "AGCGGCCAGCTGCCTGAA"
mylen <- 5 
ss <- strsplit(x, "")[[1]]
sapply(split(ss, ceiling(seq_along(ss)/mylen)), paste, collapse = "")

Substrings of whole string in R

2 Answers2