Here is how the data files contained in this package were produced:

1) Choose a <DOWNLOAD_DIR> dir e.g.
     ~/BSgenome_srcdata/BSgenome.Scerevisiae.UCSC.sacCer1/
   and create 2 subdirs in it: <DOWNLOAD_DIR>/seqs/ and <DOWNLOAD_DIR>/masks/

2) Download the sequence file to the <DOWNLOAD_DIR>/seqs/ dir:

     ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer1/bigZips/
       chromFa.zip (3.7M)

   and extract them:

     cd <DOWNLOAD_DIR>/seqs/
     unzip chromFa.zip

3) Download the masks files to the <DOWNLOAD_DIR>/masks/ dir:

     There are no masks files available at
       http://hgdownload.cse.ucsc.edu/goldenPath/sacCer1/

4) Install the BSgenome.Scerevisiae.UCSC.sacCer1 package (contains no data yet):

     R CMD INSTALL BSgenome.Scerevisiae.UCSC.sacCer1

5) R commands:

     library(BSgenome.Scerevisiae.UCSC.sacCer1)
     download_dir <- "<DOWNLOAD_DIR>"
     extdata_dir <- "<EXTDATA_DIR>"
     data_dir <- "<DATA_DIR>"
     system.time({
       srcdir <- file.path(download_dir, "seqs")
       forgeSeqFiles(srcdir, extdata_dir, seqnames(Scerevisiae),
                     prefix="", suffix=".fa")
       srcdir <- file.path(download_dir, "masks")
       forgeMaskFiles(srcdir, data_dir, seqnames(Scerevisiae), extdata_dir, 1, NA)
     })

