Zenbu.md

Upload to the Zenbu genome browser.

This page shows how we loaded the aligned data on the "Zenbu" genome browser. It is provided as a simple Markdown file for reference because the upload had to be done only once. We are currently improving and generalising the commands below ease and automate browser uploads with knitr.

For these commands to work, the user needs to have configured the tool zenbu_upload (available from Zenbu version 2.9.1). Here we upload on RIKEN's main public server, in a collaboration that we use to privately manage our open data. In order to reuse the code below, one would need to create one own's collaboration, or to directly upload to the "public" collaboration.

ZENBU_COLLAB <- "BLFNw_m6NRVgdC2XaT2NcB"

Accessory functions

Ad-hoc wrapper to the shell command zenbu_upload

zenbuUpload <- function ( ...
                        , URL="http://fantom.gsc.riken.jp/zenbu"
                        , verbose=FALSE
                        , echo=FALSE
                        , stdout=TRUE) {
  zenbu <- 'zenbu_upload'
  url <- c('-url', URL)
  args <- sapply(c(url, ...), shQuote)
  if (verbose == TRUE) print(paste(c(zenbu, args), collapse=' '))
  if (echo    == FALSE) {
      system2(zenbu, args, stdout=stdout)
  } else {
      system2('echo', c(zenbu, args), stdout=stdout)
  }
}

To convert from file name to sample name.

bedToSample <- function(BED)
  BED %>%
    sub("RunA", RunA, .) %>%
    sub("RunB", RunB, .) %>%
    sub(".bed", "", .) %>%
    sub("_R1", "", .)

To produce a string of keywords that will uniquely identify a sample.

standardDescription <- function(BED)
  paste( LIBRARY
       , BED %>% bedToSample
       , "C1-CAGE-preview"
       , "CAGEscan_fragments"
       , "KnitrUpload")

To upload CAGEscan fragments, only if they have not yet been uploaded.

safeZupload <- function (BED) {
  # Warning: the "notFound" function ignores queued uploads...
  notFound <- function(BED)
    zenbuUpload( "-list", "-filter", standardDescription(BED)) %>%
      tail(1) %>%
      grepl ("0 uploads --- 0 featuresources --- 0 experiments --- \\[0 total sources\\]", .)
  if(notFound(BED))
    zenbuUpload( "-file",        paste0("output/cagescan_fragments/", BED)
               , "-name",        BED  %>% sub(".bed", "", .)
               , "-assembly",    "hg38"
               , "-desc",        standardDescription(BED)
               , "-collab_uuid", ZENBU_COLLAB
               , "-singletag_exp"
               , stdout="")
}

Functions to add metadata tags.

zenbuTag <- function (filter, key, value, mode='add', ...) {
  args <- c('-mdedit', filter, mode, key, value)
  zenbuUpload (args, ...)
}

tagError <- function(BED)
  zenbuTag( standardDescription(BED)
          , 'cellomics'
          , libs[bedToSample(BED), "Error"] %>% as.character)

tagRun <- function(BED)
  zenbuTag( standardDescription(BED)
          , 'Run'
          , libs[bedToSample(BED), "Run"] %>% as.character)

tagMeta <- function(BED, TAG)
  zenbuTag( standardDescription(BED)
          , TAG
          , libs[bedToSample(BED), TAG] %>% as.character)

Zenbu uploads and tagging

samplesToUpload <- rownames(libs) %>%
  sub(RunA, "RunA", .) %>%
  sub(RunB, "RunB", .) %>%
  sub("$", "_R1.bed", .)

sapply(samplesToUpload, safeZupload)
sapply(samplesToUpload, tagError)
sapply(samplesToUpload, tagGroup)
sapply(samplesToUpload, tagMeta, TAG="Run")
sapply(samplesToUpload, tagMeta, TAG="row")
sapply(samplesToUpload, tagMeta, TAG="column")