#Post-process FaMoz Results from MyKiss
rm(list = ls())
library(plyr)

juv_file <- 	"~/sim_offspring.txt"
respar_file <- 	"~/sim_respar.txt"

Postprocess.Famoz <- function (respar_file, juv_file) {
	respar <- read.table(respar_file, header=TRUE, sep="\t", dec=".", strip.white=TRUE, colClasses = c("character", "character", "character"))
	juveniles <- read.table(juv_file, header=TRUE, sep="", strip.white=TRUE)
	output <- matrix(nrow = nrow(juveniles), ncol = 6)

for (i in 1:nrow(juveniles)) {
	output[i,1] <- as.character(juveniles$OffspringID[i])
	output[i,2] <- as.character(lapply(strsplit(output[i,1], "__"), "[", 2))
	output[i,2] <- as.character(lapply(strsplit(output[i,2], "x"), "[", 1))
	output[i,3] <- as.character(lapply(strsplit(output[i,1], "x"), "[", 2))
	output[,4] <- as.character(respar$parent1[match(output[,1], respar$OffspringID)])
	output[,5] <- as.character(respar$parent2[match(output[,1], respar$OffspringID)])
	output[,4][is.na(output[,4])] <- "no ass"
	output[,5][is.na(output[,5])] <- "no ass"

	if(output[i,4] == "no ass" & output[i,5] == "no ass") { 						# EXCLUSION
		if(output[i,2] == "Unk" & output[i,3] == "Unk") {
			output[i,6] <- "12_____TRUE.X"
		} else {
			if(output[i,2] == "Unk" | output[i,3] == "Unk") {
				output[i,6] <- "13_____beta-1"	
			} else {
				output[i,6] <- "14_____beta-2"	
			}
		}
	} else {
		if(output[i,4] != "no ass" & output[i,5] != "no ass") {						# ASSIGN. PAIR
			if(output[i,4] == output[i,2] & output[i,5] == output[i,3]) {
				output[i,6] <- "06_____TRUE.P"
			} else {
				if(output[i,4] != output[i,2] & output[i,5] != output[i,3]) { 			# Both parents false
					if(output[i,2] == "Unk" & output[i,3] == "Unk") {
						output[i,6] <- "11__alpha-2pp"
					} else {
						if(output[i,2] != "Unk" & output[i,3] != "Unk") {
							output[i,6] <- "10_alpha-1pp2"	
						} else {
							if(output[i,2] != "Unk" | output[i,3] != "Unk") {
								output[i,6] <- "09_alpha-1pp1"
							}
						}
					}
				} else {
					if(output[i,2] == "Unk" | output[i,3] == "Unk") {					# One parent false
						output[i,6] <- "08___alpha-2p"
					} else {
						output[i,6] <- "07___alpha-1p"
					}
				}
			}
		} else {
			if(output[i,4] == "no ass" | output[i,5] == "no ass") {					# ASSIGN. SINGLE
				if(output[i,4] == output[i,2] | output[i,5] == output[i,3]) {			# True assignment
					if(output[i,2] == "Unk" | output[i,3] == "Unk"){
						output[i,6] <- "01_____TRUE.S"
					} else {
						output[i,6] <- "02_______beta"
					}
				} else {
					if(output[i,2] == "Unk" & output[i,3] == "Unk") {					# False assignment
						output[i,6] <- "05___alpha-2s"
					} else {
						if(output[i,2] != "Unk" & output[i,3] != "Unk") {
							output[i,6] <- "04__alpha-1s2"
						} else {
							if(output[i,2] != "Unk" | output[i,3] != "Unk") {
								output[i,6] <- "03__alpha-1s1"
							} else {
								output[i,6] <- "UNDEFINED"
							}
						}
					}
				}
			}
		}
	}
}

df <- as.data.frame(output[sort.list(output[,6], decreasing = FALSE), ])
names(df) <- c("Offspring", "True.M","True.F", "Ass.F", "Ass.M", "category")

cat.count <- as.data.frame(ddply(df, 'category', function(x) count=nrow(x)))
names(cat.count) <- c("category", "count")

known.pairs <- length(which(df$True.M != "Unk" & df$True.F != "Unk"))
known.singles <- length(which(df$True.M != "Unk" | df$True.F != "Unk")) - known.pairs
known.exclusions <- length(which(df$True.M == "Unk" & df$True.F == "Unk"))
true.accuracy <- length(which(df$category == "01_____TRUE.S" | df$category == "06_____TRUE.P" | df$category =="12_____TRUE.X")) / nrow(juveniles)

print(subset(df, df$category != "01_____TRUE.S" & df$category != "06_____TRUE.P" & df$category != "12_____TRUE.X"))
print(cat.count)
print(c(paste("known singles =", known.singles), paste("known pairs =", known.pairs), paste("known exclusions =", known.exclusions)))
print(paste("Overall accuracy =", true.accuracy))
}

Postprocess.Famoz(respar_file, juv_file)