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rstringdataframedplyrcharacter

Finding the longest stretch of repeated words in a long string of characters

I have a long DNA sequence text file with characters (ATCG). I am looking for some method in R that can be used to find the longest stretch with repeated words. Lets say my string looks like, AAGTGCGGGTTCAGATCGCCCCCCCATCGGGCAAAAAAAAAAAAAAAATCGA

I need the output possibly with counts, AAAAAAAAAAAAAAAA n=16

Please help me with this.

Solution

  • if you have one string:

    library(tidyverse)
string <- "AAGTGCGGGTTCAGATCGCCCCCCCATCGGGCAAAAAAAAAAAAAAAATCGA"

x <- str_extract_all(string, "(.)\\1+")
x[which.max(nchar(x))]

[1] "AAAAAAAAAAAAAAAA"

    if you have many strings:

    str_extract_all(c(string, string), "(.)\\1+")%>%
  map_chr(~.x[which.max(nchar(.x))])

[1] "AAAAAAAAAAAAAAAA" "AAAAAAAAAAAAAAAA"

    To find the counts, just use nchar or even str_count of the result