#' @export
CalcAlleleDiffs <- function(f){
infoTable <- as.matrix(read.csv(f, header=TRUE))
BEG1 <- as.numeric(infoTable[1,2])
END1 <- as.numeric(infoTable[2,2])
str1 <- toString(infoTable[4,2])
for(j in BEG1:END1){
filePath <- paste(c(str1,"/I",j,"/I",j,"_allelesFromPost_4.txt"), collapse = "")
if (file.exists(filePath) == TRUE){
outFilePath <- paste(c(str1,"/I",j,"/I",j,"_allelesFromPost_4_diffs.txt"), collapse = "")
outTable <- matrix(nrow = 1, ncol = 8)
k <-scan(filePath, sep = ">", what = "complex")
for(i in seq(2,length(k),12)){
textMat <- matrix(nrow = 6, ncol = 8)
allele <- strsplit(k[i],".", fixed = TRUE)
locus <- strsplit(allele[[1]][1],"L")[[1]][2]
copy <- allele[[1]][2]
alleleNumber <- allele[[1]][3]
a1 <- k[i+1]
a2 <- k[i+4]
a3 <- k[i+7]
a4 <- k[i+10]
textMat[,c(1,4)] <- locus
textMat[,c(2,5)] <- copy
textMat[,3] <- c(1,1,1,2,2,3)
textMat[,6] <- c(2,3,4,3,4,4)
textMat[,7] <- c(adist(a1,a2),adist(a1,a3), adist(a1,a4), adist(a2,a3), adist(a2,a4), adist(a3,a4))
textMat[,8] <- nchar(a1)
outTable <- rbind(outTable,textMat)
}
outTable <- outTable[2:length(outTable[,1]),]
write.table(outTable,file = outFilePath, quote = FALSE, sep = "\t", row.names = FALSE, col.names = FALSE)
print(j)
}
else {
print(paste(c("I",j," FILE NOT FOUND"), collapse = ""), quote = FALSE)
}
}
assign("infoTable",infoTable,globalenv())
}
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