Split into 3 character length
I have very simple question: How can I divide the following text into 3 in a single code
mycodes <- c("ATTTGGGCTAATTTTGTTTCTTTCTGGGTCTCTC")
strsplit(mycodes, split = character(3), fixed = T, perl = FALSE, useBytes = FALSE)
[[1]]
[1] "A" "T" "T" "T" "G" "G" "G" "C" "T" "A" "A" "T" "T" "T" "T" "G" "T" "T" "T" "C"
[21] "T" "T" "T" "C" "T" "G" "G" "G" "T" "C" "T" 开发者_开发百科"C" "T" "C"
This is not what I want; I want three letters at a time:
[1] "ATT" "TGG", "GCT"...............and so on the final may be of one, two or three letters depending upon the letter availability.
Thanks;
I assume you want to work with codons. If that's the case, you might want to look at the Biostrings package from Bioconductor. It provides a variety of tools for working with biological sequence data.
library(Biostrings)
?codons
You can achieve what you want, with a little bit of clumsy coercion:
as.character(codons(DNAString(mycodes)))
Here is one approach using stringr
package
require(stringr)
start = seq(1, nchar(mycodes), 3)
stop = pmin(start + 2, nchar(mycodes))
str_sub(mycodes, start, stop)
Output is
[1] "ATT" "TGG" "GCT" "AAT" "TTT" "GTT" "TCT" "TTC" "TGG"
[10] "GTC" "TCT" "C"
You can also use:
strsplit(data, '(?<=.{3})', perl=TRUE)
[[1]]
[1] "ATT" "TGG" "GCT" "AAT" "TTT" "GTT" "TCT" "TTC" "TGG" "GTC" "TCT" "C"
or
library(stringi)
stri_extract_all_regex(data, '.{1,3}')
精彩评论