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How to extract all characters before and after a certain set of characters in R while making sure those characters are first/last in the string?

I have a long string:

my_string = "GTCAGTCGATCTGGGCATTATGCGTCAAAAGGCTGCTAGCTAAAGCTGATCAGCATCAAAAGGCCGCCCCTATGCTACGAGCATCATGCATCTGGGTCTAGCTAGTGGGCATTCTCTCTGCTGCATTCAGTCACAAAAGGTGTCAGTCGTAGTCATCATCTACATCGTTCATGCTGGGCATTACAGTCAGTCACAAAAGGTCAGTCAGTCA"

I want to extract two things from this string:

  1. Everything "before" the first encountered CAAAAG
  2. Everything "after" the last encountered TGGGCATT

Everything before CAAAAG can be found like this:

stringr::word(my_string, 1, sep = "CAAAAG")

But how do I make sure that it is "first" CAAAAG in the string? And that I am receiving all characters found before the very first CAAAAG?

The same goes for TGGGCATT. I can receive everything "after" TGGGCATT in this way:

stringr::word(my_string, -1, sep = "TGGGCATT")

But how do I make sure that I am getting all characters coming "after" the LAST TGGGCATT in my string?

Solution

  • I think I've got two ways that I used for each. 

    my_string = "GTCAGTCGATCTGGGCATTATGCGTCAAAAGGCTGCTAGCTAAAGCTGATCAGCATCAAAAGGCCGCCCCTATGCTACGAGCATCATGCATCTGGGTCTAGCTAGTGGGCATTCTCTCTGCTGCATTCAGTCACAAAAGGTGTCAGTCGTAGTCATCATCTACATCGTTCATGCTGGGCATTACAGTCAGTCACAAAAGGTCAGTCAGTCA"

library(stringr)

str_match_all(my_string, '(.*?)CAAAAG')

#[[1]]
#     [,1]                                                                           
#[1,] "GTCAGTCGATCTGGGCATTATGCGTCAAAAG"                                              
#[2,] "GCTGCTAGCTAAAGCTGATCAGCATCAAAAG"                                              
#[3,] #"GCCGCCCCTATGCTACGAGCATCATGCATCTGGGTCTAGCTAGTGGGCATTCTCTCTGCTGCATTCAGTCACAAAAG"
#[4,] "GTGTCAGTCGTAGTCATCATCTACATCGTTCATGCTGGGCATTACAGTCAGTCACAAAAG"                 
#     [,2]                                                                     
#[1,] "GTCAGTCGATCTGGGCATTATGCGT"                                              
#[2,] "GCTGCTAGCTAAAGCTGATCAGCAT"                                              
#[3,] "GCCGCCCCTATGCTACGAGCATCATGCATCTGGGTCTAGCTAGTGGGCATTCTCTCTGCTGCATTCAGTCA"
#[4,] "GTGTCAGTCGTAGTCATCATCTACATCGTTCATGCTGGGCATTACAGTCAGTCA"  

first.match <- str_match_all(my_string, '(.*?)CAAAAG')[[1]][1,2]
first.match
#[1] "GTCAGTCGATCTGGGCATTATGCGT"

str_locate_all(my_string, 'TGGGCATT')
#[[1]]
#     start end
#[1,]    12  19
#[2,]   106 113
#[3,]   175 182
second.match.index <- str_locate_all(my_string, 'TGGGCATT')[[1]]
second.match <- substr(my_string,second.match.index[nrow(second.match.index),ncol(second.match.index)]+1,
                       nchar(my_string))

second.match
#[1] "TACAGTCAGTCACAAAAGGTCAGTCAGTCA"

    Edit: Added '+1' because you want the very next index, not the one where the searched string ends.