HI,
I am sorry. I didn't test it properly.
Check if this works. (But, you already got Hervé's solution).
For ##2
eyaSpl2 <- rep("#",sum(length(eyaSpl),length(CDS1[,1]))) ##as in previous code
indx <- CDS1[,1]+rep(seq(0,length(CDS1[,1]),by=2),each=2)[-c(1,40)]
eyaSpl2[-indx] <- eyaSpl
###testing
indx2 <- which(eyaSpl2=="#")
lst1 <- lapply(split(CDS1[,1],((seq_along(CDS1[,1])-1)%/%2)+1),function(x)
paste(eyaSpl[(x[1]-1):(x[2]+1)],collapse=""))
lst2 <- lapply(split(indx2,((seq_along(indx2)-1)%/%2)+1),function(x)
paste(eyaSpl2[(x[1]-1):(x[2]+1)],collapse=""))
lst1[[1]]
#[1] "fapkkaakafmfffakkannpaaapkacfaapfdk"
lst2[[1]]
#[1] "f#apkkaakafmfffakkannpaaapkacfaapfd#k"
####
lst1[[2]]
#[1] "kkpaaakaaaafkpkfbfakaaofakapkpppfcgaanfpfakaappffakk"
lst2[[2]]
#[1] "k#kpaaakaaaafkpkfbfakaaofakapkpppfcgaanfpfakaappffak#k"
####
lst1[[19]]
#[1]
"kfafaafapkfffpphpkkakkapapfeaknfafpfckaffpfhpkkfpfpefahfaakfafpkkaappakakpapppkpaaf"
lst2[[19]]
#[1]
"k#fafaafapkfffpphpkkakkapapfeaknfafpfckaffpfhpkkfpfpefahfaakfafpkkaappakakpapppkpaa#f"
A.K.
Hi A.K., thanks for your help. I have some follow up queries.
For ##2, the code doesn't seem to get exactly what I was after. For example,
for the first position pair, the code generates:
a#fapkkaakafmfffakkannpaaapkacfaapf#dk
whereas the # signs should be around this:
af#apkkaakafmfffakkannpaaapkacfaapfd#k
The positions of # are also slightly off for the latter position pairs.
On Thursday, January 23, 2014 2:04 PM, arun <smartpink...@yahoo.com> 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.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
