UCSC table to GRanges object (only chrom, start and end)

ucsctable2gr.R

uniform_tfbs = data.frame(cell.line=c("GM12878" ,"H1-hESC" ,"K562", "HeLa-S3", "HepG2", "HUVEC", "A549", "IMR-90",	"MCF-7"),
                          schema=c("wgEncodeAwgTfbsUtaGm12878CtcfUniPk", "wgEncodeAwgTfbsUtaH1hescCtcfUniPk", "wgEncodeAwgTfbsUtaK562CtcfUniPk", "wgEncodeAwgTfbsUtaHelas3CtcfUniPk",
                                   "wgEncodeAwgTfbsUtaHepg2CtcfUniPk", "wgEncodeAwgTfbsUtaHuvecCtcfUniPk", "wgEncodeAwgTfbsHaibA549Ctcfsc5916Pcr1xDex100nmUniPk",
                                   "wgEncodeAwgTfbsSydhImr90CtcfbIggrabUniPk", "wgEncodeAwgTfbsUtaMcf7CtcfSerumstimUniPk"),
                          stringsAsFactors = FALSE)


#' UCSC table to GRanges object (only chrom, start and end)
#' 
#' @param table UCSC table
#' @param assembly genome assembly
UCSCtable2Granges = function(table, assembly="hg19"){
  require(RMySQL)
  require(GenomicRanges)
  con <- dbConnect(MySQL(),user="genome",db=assembly,host="genome-mysql.cse.ucsc.edu")
  query = dbSendQuery(con, paste0("SELECT chrom, chromStart, chromEnd FROM ", assembly, ".", table));
  res = fetch(query, n=-1); # n = -1 to retrieve all pending records. 
  dbClearResult(query)
  dbDisconnect(con)
  makeGRangesFromDataFrame(res,
                           seqnames.field="chrom", start.field="chromStart", end.field="chromEnd")
}

uniform_tfbs_schemas_gr = mclapply(uniform_tfbs$schema, 
                                   function(table){
                                     print(table)
                                     UCSCtable2Granges(table, "hg19")
                                   },
                                   mc.cores=9)
names(uniform_tfbs_schemas_gr) = uniform_tfbs$cell.line