TwoBitFile-class: 2bit Files

Description

These functions support the import and export of the UCSC 2bit compressed sequence format. The main advantage is speed of subsequence retrieval, as it only loads the sequence in the requested intervals. Compared to the FA format supported by Rsamtools, 2bit offers the additional feature of masking and also has better support in Java (and thus most genome browsers). The supporting TwoBitFile class is a reference to a TwoBit file.

Usage

"import"(con, format, text, which = as(seqinfo(con), "GenomicRanges"), ...)
"getSeq"(x, which = as(seqinfo(con), "GenomicRanges"))
import.2bit(con, ...)
"export"(object, con, format, ...)
"export"(object, con, format)
"export"(object, con, format, ...)
export.2bit(object, con, ...)

Arguments

con

A path, URL or TwoBitFile object. Connections are not supported. For the functions ending in .2bit, the file format is indicated by the function name. For the export and import methods, the format must be indicated another way. If con is a path, or URL, either the file extension or the format argument needs to be “twoBit” or “2bit”.

object,x

The object to export, either a DNAStringSet or something coercible to a DNAStringSet, like a character vector.

format

If not missing, should be “twoBit” or “2bit” (case insensitive).

text

Not supported.

which

A range data structure coercible to RangesList, like a GRanges, or a TwoBitFile. Only the intervals in the file overlapping the given ranges are returned. By default, the value is the TwoBitFile itself. Its Seqinfo object is extracted and coerced to a RangesList that represents the entirety of the file.

...

Arguments to pass down to methods to other methods. For import, the flow eventually reaches the TwoBitFile method on import. For export, the TwoBitFile methods on export are the sink.

Value

For import, a DNAStringSet.

<code>TwoBitFile</code> objects

A TwoBitFile object, an extension of RTLFile is a reference to a TwoBit file. To cast a path, URL or connection to a TwoBitFile, pass it to the TwoBitFile constructor. A TwoBit file embeds the sequence information, which can be retrieved with the following:

: seqinfo(x): Gets the Seqinfo object indicating the lengths of the sequences for the intervals in the file. No circularity or genome information is available.

Examples

Run this code

  test_path <- system.file("tests", package = "rtracklayer")
  test_2bit <- file.path(test_path, "test.2bit")

  test <- import(test_2bit)
  test

  test_2bit_file <- TwoBitFile(test_2bit)
  import(test_2bit_file) # the whole file
  
  which_range <- IRanges(c(10, 40), c(30, 42))
  which <- GRanges(names(test), which_range)
  import(test_2bit, which = which)

  seqinfo(test_2bit_file)

## Not run: 
#   test_2bit_out <- file.path(tempdir(), "test_out.2bit")
#   export(test, test_2bit_out)
# 
#   ## just a character vector
#   test_char <- as.character(test)
#   export(test_char, test_2bit_out)
# ## End(Not run)