Deleting subsequences and inserting strings into a sequence - r

Question

I have a data file here, which is imported into R by:
eya4_lagan_HM_cp <- "E:/blahblah/eya4_lagan_HM_cp.txt"
eya4_lagan_HM_cp <- readChar(eya4_lagan_HM_cp, file.info(eya4_lagan_HM_cp)$size)
Label the first string with position "1" and the last string as position "311,522" (note the sequence contains in total 311,522 characters). I have two queries which are closely related.
Query 1)
Now I have a data file with a list of positions here. The positions are read in "pairs", that is, take the first pair 44184 and 44216 as an example. I wish to delete the subsequence from position 44184 (inclusive) to position 44216 (inclusive) from the previous sequence eya4_lagan_HM_cp and in its place, insert the character #. In other words, substitute the subsequence from 44184 to 44216 with #. I would like to do this with the rest of the pairs, that is, for 151795 and 151844, I want to delete from position 151795 (inclusive) to 151844 (inclusive) in eya4_lagan_HM_cp and replace it with #, and so on.
Query 2)
Now I would like to do something slightly different with the data file with the list of positions. Take the first pair as an example again. I would like to insert a # right before position 44184, in other words, insert a # between positions 44183 and 44184 in eya4_lagan_HM_cp and then I would like to insert a # right after position 44216, i.e., insert a # between positions 44216 and 44217. I would like to repeat this procedure for all position pairs. So for the next pair, I would like a # right before 151795 and a # right after 151844.
Thank you.

Answer 1

e <- eya4_lagan_HM_cp <- readChar("eya4_lagan_HM_cp.txt", file.info("eya4_lagan_HM_cp.txt")$size)
pairs <- as.numeric(readLines("CDS coordinates.txt"))
idx1 <- pairs[seq(1, length(pairs), 2)]
idx2 <- pairs[seq(2, length(pairs), 2)]
e.split <- strsplit(e, "")[[1]]
# no1
hashIndices <- unlist(mapply(seq, from=idx1, to=idx2))
e.split[hashIndices] <- "#"
e.new <- paste(e.split, collapse="")
# no2
for (idx in c(idx1, idx2+1))
e.split <- c(e.split[1:(idx-1)], "#", e.split[idx:length(e.split)])
e.new <- paste(e.split, collapse="")
Edit:
Another try with reference to the comment: After e.split <- strsplit(e, "")[[1]] either
# no1
deleteIndices <- unlist(mapply(seq, from=idx1+1, to=idx2))
e.split[idx1] <- "#"
e.new <- paste(e.split[-deleteIndices], collapse="")
or
# no2
for (idx in c(idx1, idx2+2))
e.split <- c(e.split[1:(idx-1)], "#", e.split[idx:length(e.split)])
e.new <- paste(e.split, collapse="")

Answer 2

If you can assume the strings that are being replaced are unique, you might try a combination of substr() and gsub(). (If you only had to do the replacement once, you would only need substr.) For example if you loaded your pairs of positions into a 2-column matrix pp your query 1 could be
for(i in 1:nrow(pp)) {
ss <- substr(eya4_lagan_HM_cp,start=pp[i,1],stop=pp[i,2])
eya4_lagan_HM_cp = gsub(ss,"#",eya4_lagan_HM_cp)
}
and query 2
for(i in 1:nrow(pp)) {
ss <- substr(eya4_lagan_HM_cp,start=pp[i,1],stop=pp[i,2])
eya4_lagan_HM_cp <- gsub(ss,paste("#",ss,"#",sep=""),eya4_lagan_HM_cp)
}
If you can't assume the strings to be replaced will be unique, you could explode out the string eya4_lagan_HM_cp into a vector of character strings:
vv <-unlist(strsplit(eya4_lagan_HM_cp,split=""))
use vector subsetting to remove/insert, e.g., for query 1,
new.vv <- c(vv[1:(pp[1,1]-1)],"#")
for(i in 1:(nrow(pp)-1)) {
new.vv <-c(new.vv,vv[(pp[i,2]+1):(pp[(i+1),1]-1)],"#")
}
new.vv <- c(new.vv,vv[(pp[2,nrow(pp)]+1):length(vv)])
and then paste back together as one string
eya4_lagan_HM_cp <- paste(new.vv,sep="")