suppressMessages(library(tidyverse))
suppressMessages(library(clusterProfiler))


args <- commandArgs()

out.dir <- args[6]
pval  <- as.numeric(args[7])
qval  <- as.numeric(args[8])
db <- args[9]
gene_type <- args[10]
org_db <- args[11]
kegg_org <- args[12]
dpsi_file <- args[13]

suppressMessages(library(org_db, character.only = T))

script_path  <- str_split(args[4], "=")[[1]][2]
source(file.path(dirname(script_path), "utils.R"))

# dpsi_file <- "output/fb_e10/sig/2_SE.sig.dpsi"
# out.dir <- "output/fb_e10/enrich/1_SE.sig"
# org_db <- org.Mm.eg.db
# pval <- 0.1
# qval <- 0.1
# gene_type <- "ENSEMBL"
# source("/home/huangshenghui/project/asla/laas/R/utils.R")




dpsi <- read_tsv(dpsi_file, skip =1, col_names = F,
                col_types = cols("c", "d", "d"))

colnames(dpsi) = c("event_id", "dpsi", "pval")

genes <- gsub("\\..*", "",  dpsi$event_id) 

if (db == "GO"){
    enrichGOSep(genes, out.dir,
            org_db, name="GO",
            keyType = gene_type,
            pval = pval, qval = qval)
}else if (db == "KEGG") {
   enrichKEGGSep(genes, out.dir, org_db, name = "KEGG",
                        org = kegg_org, keytype = gene_type,
                        pval = pval, qval = qval)
}
