--- a
+++ b/4-Multi-Omic Integration/scripts/4.KO2metabo.r
@@ -0,0 +1,39 @@
+# 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 = ""))