Dmelanogasterpackage:BSgenome.Dmelanogaster.UCSC.dm2R Documentation

_D_r_o_s_o_p_h_i_l_a _m_e_l_a_n_o_g_a_s_t_e_r _f_u_l_l _g_e_n_o_m_e (_U_C_S_C _v_e_r_s_i_o_n _d_m_2)

_D_e_s_c_r_i_p_t_i_o_n:

     Drosophila melanogaster full genome as provided by UCSC (dm2, Apr.
     2004) and stored in Biostrings objects.

_N_o_t_e:

     This BSgenome data package was made from the following source data
     files:


     sequences: chromFa.zip, upstream1000.fa.gz, upstream2000.fa.gz,
     upstream5000.fa.gz
     from http://hgdownload.cse.ucsc.edu/goldenPath/dm2/bigZips/
     masks: all the chr*_gap.txt.gz files from
     ftp://hgdownload.cse.ucsc.edu/goldenPath/dm2/database/
     + chromOut.zip and chromTrf.zip from
     http://hgdownload.cse.ucsc.edu/goldenPath/dm2/bigZips/

     See '?BSgenomeForge' and the BSgenomeForge vignette
     ('vignette("BSgenomeForge")') in the BSgenome software package for
     how to make a BSgenome data package.

_A_u_t_h_o_r(_s):

     H. Pages

_S_e_e _A_l_s_o:

     BSgenome-class, DNAString-class, 'available.genomes',
     BSgenomeForge

_E_x_a_m_p_l_e_s:

     Dmelanogaster
     seqlengths(Dmelanogaster)
     Dmelanogaster$chr2L  # same as Dmelanogaster[["chr2L"]]

     if ("AGAPS" %in% masknames(Dmelanogaster)) {

       ## Check that the assembly gaps contain only Ns:
       checkOnlyNsInGaps <- function(seq)
       {
         ## Replace all masks by the inverted AGAPS mask
         masks(seq) <- gaps(masks(seq)["AGAPS"])
         af <- alphabetFrequency(seq)
         found_letters <- names(af)[af != 0]
         if (any(found_letters != "N"))
             stop("assembly gaps contain more than just Ns")
       }

       ## A message will be printed each time a sequence is removed
       ## from the cache:
       options(verbose=TRUE)

       for (seqname in seqnames(Dmelanogaster)) {
         cat("Checking sequence", seqname, "... ")
         seq <- Dmelanogaster[[seqname]]
         checkOnlyNsInGaps(seq)
         cat("OK\n")
       }
     }

     ## See the GenomeSearching vignette in the BSgenome software
     ## package for some examples of genome-wide motif searching using
     ## Biostrings and the BSgenome data packages:
     if (interactive())
         vignette("GenomeSearching", package="BSgenome")

