R/fasta.R

In rtracklayer: R interface to genome annotation files and the UCSC genome browser

### =========================================================================
### FASTA support
### -------------------------------------------------------------------------
###
### Since we have 2bit, we might as well have FASTA
###

setClass("FastaFile", contains = "RTLFile")

FastaFile <- function(resource) {
  new("FastaFile", resource = resource)
}

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### Export
###

setMethod("export", c("ANY", "FastaFile"), function(object, con, ...) {
  export(as(object, "DNAStringSet"), con, ...)
})

setMethod("export", c("XStringSet", "FastaFile"),
          function(object, con, format, ...)
          {
            writeXStringSet(object, path(con), format = "fasta", ...)
          })

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### Import
###

setMethod("import", "FastaFile",
          function(con, format, text, type = c("DNA", "RNA", "AA", "B"), ...)
          {
            if (!missing(format))
              checkArgFormat(con, format)
            readFun <- get(paste0("read", match.arg(type), "StringSet"),
                           getNamespace("Biostrings"))
            readFun(path(con), format = "fasta", ...)
          })