library(plyr)
library(dplyr)

# inputFile <- "diffbind/DBA_Sham-YOUNG_vs_Bleo-YOUNG.diffbind.p1f0.all.sigsites.annotated.tsv"
# prefix <- "SY_BY"

args <- commandArgs(T)
inputFile <- args[1]
prefix <- args[2]

input <- read.delim(inputFile)

nonSig <- input[which(input$p.value >= 0.05),]
Sig <- input[which(input$p.value < 0.05),]

sigUp <- Sig[which(Sig$Fold > 0),]
sigDown <- Sig[which(Sig$Fold < 0),]

flat <- Sig[which(Sig$Fold == 0),]

Up_In_Con <- sigUp
Down_In_Con <- sigDown
nonsignificant <- bind_rows(nonSig,flat)


Up_In_Con <- Up_In_Con[,c(1:3)]
Up_In_Con$Peak <- paste0("peak_",seq(1:nrow(Up_In_Con)))
Up_In_Con$Score <- "."
Up_In_Con$Strand <- "."



Down_In_Con <- Down_In_Con[,c(1:3)]
Down_In_Con$Peak <- paste0("peak_",seq(1:nrow(Down_In_Con)))
Down_In_Con$Score <- "."
Down_In_Con$Strand <- "."


nonsignificant <- nonsignificant[,c(1:3)]
nonsignificant$Peak <- paste0("peak_",seq(1:nrow(nonsignificant)))
nonsignificant$Score <- "."
nonsignificant$Strand <- "."


write.table(Up_In_Con,paste0(prefix,"_UpInCon.bed"),sep = "\t",quote = F,row.names = F,col.names = F)
write.table(Down_In_Con,paste0(prefix,"_DownInCon.bed"),sep = "\t",quote = F,row.names = F,col.names = F)
write.table(nonsignificant,paste0(prefix,"_NS.bed"),sep = "\t",quote = F,row.names = F,col.names = F)