According to the OP
Later on I wish to turn longer sub-sequences into sequences of 1's,
such as 10001 to 11111.
If I understand correctly, the final goal is to replace any sub-sequence of consecutive 0 into the same number of 1 if they are surrounded by a 1 on both sides.
In R, this can be achieved by the str_replace_all() function from the stringr package. For demonstration and testing, the input vector contains some edge cases where substrings of 0 are not surrounded by 1.
input <- c("110101101",
"11010110001",
"110-01101",
"11010110000",
"00010110001")
library(stringr)
str_replace_all(input, "(?<=1)0+(?=1)", function(x) str_dup("1", str_length(x)))
[1] "111111111" "11111111111" "110-01111" "11111110000" "00011111111"
The regex "(?<=1)0+(?=1)" uses look behind (?<=1) as well as look ahead (?=1) to ensure that the subsequence 0+ to replace is surrounded by 1. Thus, leading and trailing subsequences of 0 are not replaced.
The replacement is computed by a functions which returns a subsequence of 1 of the same length as the subsequence of 0 to replace.