Getting mitopathways into GMT format

mitopathways.R

library(rvest)
library(dplyr)

url="https://www.broadinstitute.org/files/shared/metabolism/mitocarta/human.mitocarta3.0.path_.html"

webpage <- read_html(url)

tbls <- html_nodes(webpage, "table")


tbl <- webpage %>%  html_nodes("table") %>% .[1] %>% html_table(fill = TRUE)

tbl <- tbl[[1]]

colnames(tbl) <- c("pathway","description","set")

df <- as.data.frame(tbl)

sets <- strsplit(df$set,",")

sets <- lapply(sets, function(v) { gsub(" ","",v) } )

names(sets) <- paste(df[,1],df[,2])

writeGMT <- function (object, fname ){
  if (class(object) != "list") stop("object should be of class 'list'")
  if(file.exists(fname)) unlink(fname)
  for (iElement in 1:length(object)){
    write.table(t(c(make.names(rep(names(object)[iElement],2)),object[[iElement]])),
                sep="\t",quote=FALSE,
                file=fname,append=TRUE,col.names=FALSE,row.names=FALSE)
  }
}


writeGMT(object=sets,fname="mitopathways.gmt")