# files required:
# 1) "cmpd2metabo.txt" storing compound IDs and corresponding compound names
# 2) "KO2CMPD.lists.RData" generated from script "4.KO2cmpd.r" 

# output:
# "KO2METABO.lists.RData" stored in the "database" directory



library(data.table)

##  generate KO.Substrates.metab, KO.Products.metab and KO.SubsProd.metab lists
dbDir = "database"
cpmd2metab <- fread(paste(dbDir,"/cmpd2metabo.txt",sep = ""),data.table = F )
load(paste(dbDir,"/KO2CMPD.lists.RData",sep = ""))

KO.Substrates.metab_list <-  vector("list", length = length(KO.Substrates_list))
KO.Products.metab_list <-  vector("list", length = length(KO.Substrates_list))
KO.SubsProd.metab_list <-  vector("list", length = length(KO.Substrates_list))

for(i in c(1:length(KO.Substrates_list))){
  
  ko <- names(KO.Substrates_list)[i]
  
  substrates <- KO.Substrates_list[[ko]]
  products <- KO.Products_list[[ko]]
  subs.prod <- KO.SubsProd_list[[ko]]
  
  substrates.metab <- unlist(sapply(substrates, function(x) cpmd2metab$Metabolome[cpmd2metab$MetaCyc_compounds == x]))
  products.metab <- unlist(sapply(products, function(x) cpmd2metab$Metabolome[cpmd2metab$MetaCyc_compounds == x]))
  subs.prod.metab <- unlist(sapply(subs.prod, function(x) cpmd2metab$Metabolome[cpmd2metab$MetaCyc_compounds == x]))
  
  if(!is.null(substrates.metab) & length(substrates.metab) > 0 )  KO.Substrates.metab_list[[i]] <- substrates.metab; names(KO.Substrates.metab_list)[i] <- ko
  if(!is.null(products.metab) & length(products.metab) > 0 )  KO.Products.metab_list[[i]] <- products.metab; names(KO.Products.metab_list)[i] <- ko
  if(!is.null(subs.prod.metab) & length(subs.prod.metab) > 0 )  KO.SubsProd.metab_list[[i]] <- subs.prod.metab; names(KO.SubsProd.metab_list)[i] <- ko
}

save(KO.Products.metab_list, KO.SubsProd.metab_list, KO.Substrates.metab_list,
     file = paste(dbDir, "/KO2METABO.lists.RData",sep = ""))