Athaliana  package:BSgenome.Athaliana.TAIR.04232008  R Documentation

_A_r_a_b_i_d_o_p_s_i_s _t_h_a_l_i_a_n_a _f_u_l_l _g_e_n_o_m_e (_T_A_I_R _v_e_r_s_i_o_n _f_r_o_m _A_p_r_i_l _2_3, _2_0_0_8)

_D_e_s_c_r_i_p_t_i_o_n:

     Arabidopsis thaliana full genome as provided by TAIR (snapshot
     from April 23, 2008) and stored in Biostrings objects.

_N_o_t_e:

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


     all the chr*.fas file from
     ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/
     WARNING: This is where things are today (Oct 1st, 2008) but is
     probably
     NOT aimed to be the permanent URL for the 04232008 snapshot of the
     genome.
     TAIR might update the content of this folder in the future with a
     new
     snapshot and move the 04232008 snapshot to the OLD/ subfolder.

     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:

     Athaliana
     seqlengths(Athaliana)
     Athaliana$chr1  # same as Athaliana[["chr1"]]

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

       ## 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(Athaliana)) {
         cat("Checking sequence", seqname, "... ")
         seq <- Athaliana[[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")

