[R] Deleting subsequences from a string sequence

[Hervé Pagès]

Hi,

This is easy to do with the Biostrings package (from Bioconductor).

Let's say you've managed to load the string from your
eya4_lagan_HM_cp.txt file:

   my_seq <- "123456789012345678901234567890"

What you call "pairs of positions" are "ranges". Let's say you've
managed to the ranges from your data file:

   my_ranges <- rbind(c(3, 7), c(12, 13), c(18, 25))

Then:

   library(Biostrings)
   my_seq <- BString(my_seq)
   my_ranges <- IRanges(my_ranges[ ,1], my_ranges[ ,2])

Query 1:

   > replaceAt(my_seq, at=my_ranges, value="#")
     18-letter "BString" instance
   seq: 12#8901#4567#67890

Query 2:

   > replaceAt(my_seq, at=my_ranges, value=paste0("#", extractAt(my_seq, 
my_ranges), "#"))
     36-letter "BString" instance
   seq: 12#34567#8901#23#4567#89012345#67890

   ## Or, equivalently (but more efficiently):

   > replaceAt(my_seq, at=c(start(my_ranges), end(my_ranges) + 1), 
value="#")
     36-letter "BString" instance
   seq: 12#34567#8901#23#4567#89012345#67890

You can turn the BString objects back into ordinary strings with
as.character().

To install the Biostrings package:

   source("http://bioconductor.org/biocLite.R")
   biocLite("Biostrings")

Cheers,
H.


On 01/23/2014 11:04 AM, arun wrote:
> Hi,
> Try:
>   CDS1 <- read.table("CDS coordinates.txt",header=FALSE)
> CDS2 <- split(CDS1[,1],as.numeric(as.character(gl(nrow(CDS1),2,length=nrow(CDS1)))))
> eya4 <- readChar("eya4_lagan_HM_cp.txt",file.info("eya4_lagan_HM_cp.txt")$size)
>   eyaSpl<- head(strsplit(eya4,"")[[1]],-1)
> length(eyaSpl)
> #[1] 311522
>
> eyaSpl1 <- eyaSpl
> ##1
> for(i in seq_along(CDS2)){
> eyaSpl1[seq(CDS2[[i]][1],CDS2[[i]][2],by=1)] <- "#"
> eyaSpl1}
>
> ##2
>   eyaSpl2 <- rep("#",sum(length(eyaSpl),length(CDS1[,1])))
> vec1 <- unlist(lapply(CDS2,function(x) c(x[1]-1,x[2]+1)),use.names=FALSE)
>   eyaSpl2[-vec1] <- eyaSpl
> eyaSpl2New <- paste(eyaSpl2,collapse="")
>
> A.K.
>
>
> I have a data file here, which is imported into R by:
>
>      eya4_lagan_HM_cp <- "E:/blahblah/eya4_lagan_HM_cp.txt"
>
>      eya4_lagan_HM_cp <- readChar(eya4_lagan_HM_cp, file.info(eya4_lagan_HM_cp)$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.
>
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Hervé Pagès

Program in Computational Biology
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