R/downloadBigWigs.R

In tdhock/PeakSegPipeline: Genome-Wide Peak Prediction Using Supervised Learning and Optimal Segmentation

downloadBigWigs <- structure(function
### Download bigWig files from a trackDb file.
(trackDb.txt,
### trackDb text file.
  out.dir,
### Output directory.
  verbose=getOption("PeakSegPipeline.verbose", 1)
### Print messages?
){
  trackDb.vec <- readLines(trackDb.txt)
  f <- function(variable){
    nc::field(variable, " ", ".+")
  }
  track.dt <- nc::capture_all_str(
    trackDb.vec,
    f("track"),
    "(?:\n.+)*", #any number of lines
    "\\s+",
    f("bigDataUrl"))
  for(track.i in seq_along(track.dt$bigDataUrl)){
    track.name <- track.dt$track[track.i]
    u <- track.dt$bigDataUrl[track.i]
    dest <- file.path(out.dir, track.name, basename(u))
    if(verbose)cat(sprintf(
      "%4s / %4s tracks %s -> %s\n",
      track.i, nrow(track.dt),
      u, dest))
    dir.create(dirname(dest), showWarnings=FALSE, recursive=TRUE)
    tryCatch({
      download.file(u, dest)
    }, error=function(e){
      message(e)
    })
  }
### Nothing.
}, ex=function(){

  ## Create a trackDb.txt file with links to a few small bigWig files on GitHub.
  bigWig.part.vec <- c(
    "Input/MS010302",
    "bcell/MS010302",
    "Input/MS002201",
    "kidney/MS002201")
  repos.url <- "https://raw.githubusercontent.com/tdhock/input-test-data/master/"
  track.lines <- sprintf(
    "track %s\nbigDataUrl %s%s.bigwig\n",
    sub("/", "_", bigWig.part.vec),
    repos.url, bigWig.part.vec)
  track.dir <- tempfile()
  dir.create(track.dir)
  trackDb.txt <- file.path(track.dir, "trackDb.txt")
  cat(track.lines, sep="\n")
  writeLines(track.lines, trackDb.txt)

  ## Download the bigWig files mentioned in trackDb.txt
  if(interactive()){
    downloadBigWigs(trackDb.txt, track.dir, verbose=1)
  }

})