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####### Saint output correction for Tab-misplacements: function "new.saintoutput"
# Input: file-name of original saint interaction-output = unique-interaction table -> define path before!
# Output: corrected saint-output of interactions
### Correction SAINT output ###
saintout <- function(test) {
#require(seqinr)
test <- test[2:length(test)]
test <- strsplit(test,split="\t")
length(test)
#table(unlist(lapply(test, function(x){length(x)} ) )) #check number of columns: expected 12
lost12 <- which(is.na(unlist(lapply(test, function(x){x[12]} ) ) )) #column 12 missing
for ( i in lost12) {
a <- strsplit(test[[i]][10], split="|", fixed=TRUE)
ll <- length(a[[1]])
if (ll==1) # no ctrl counts, pure shifting of columns 11+12 to the previous ones
{test[[i]][12]<-test[[i]][11] ;
test[[i]][11]<-test[[i]][10] ;
test[[i]][10] <- NA
}
else # column 11 displaced in column 10
{
if(is.integer(a[[1]][ll])==FALSE)
{test[[i]][12]<-test[[i]][11] ;
test[[i]][11]<- a[[1]][ll] ;
g <- c2s(paste(a[[1]][-ll],sep="|",collaps=""))
test[[i]][10] <- substr(g,1,nchar(g)-1) }
else print("different case in:",i )
}
}
return(test)
}
#######
########## SAINT OUTPUT in Data Frame ##############
new.saintoutput <- function(filename){
#require(seqinr)
saint <- readLines(filename) # read original saint output
saint.out <- saintout(saint) # function to correct tab-mistakes from the original Saint output
saint.out2 <- as.data.frame(do.call("rbind",saint.out))
colnames(saint.out2) <- unlist(strsplit(readLines(filename)[1], split="\t", fixed=TRUE))
return(saint.out2)
}
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