library(graphite) ##Need to install the graphite package to load KEGG pathways

paths<- pathways('hsapiens','kegg') ##Load in all homo sapiens pathways
keep <- read.table("pathways.txt",sep='\n') ###OPTIONAL: If only certain pathways are to be converted into priors

keep<-sapply(keep$V1,tolower) ###Convert pathway names to lowercase to match KEGG
inds <- which(tolower(names(paths))%in%keep) ## Find which indices correspond to pathways to keep

goodPaths <- paths[inds] ###Select only these pathways
allGenes <- c()
dir.create("pathway_lists") ###Create a directory to store the pathways desired

###Loop through desired pathways and write them each as a file to the directory in .sif format
for (i in 1:length(goodPaths))
{
  curr <- goodPaths[[i]]
  print(curr)
  curr2 <- convertIdentifiers(curr,"SYMBOL")
  edges <-graphite::edges(curr2)
  allGenes <- c(allGenes,unique(c(unique(edges$src),unique(edges$dest))))
  edges <- edges[,c("src","dest")]
  write.table(edges,file=paste('pathway_lists/',curr@title,".txt",sep=''),row.names=FALSE,quote=FALSE,sep='\t')
}