export-methods: Export a BSgenome object as a FASTA or twoBit file

In Bioconductor/BSgenome: Software infrastructure for efficient representation of full genomes and their SNPs

Export a BSgenome object as a FASTA or twoBit file

Description

export methods for BSgenome objects.

NOTE: The export generic function and most of its methods are defined and documented in the BiocIO package. This man page only documents the 2 export methods defined in the BSgenome package.

Usage

## S4 method for signature 'BSgenome,FastaFile,ANY'
export(object, con, format, compress=FALSE, compression_level=NA, verbose=TRUE)
## S4 method for signature 'BSgenome,TwoBitFile,ANY'
export(object, con, format, ...)

Arguments

object	The BSgenome object to export.
con	A FastaFile or TwoBitFile object. Alternatively con can be a single string containing the path to a FASTA or twoBit file, in which case either the file extension or the format argument needs to be "fasta", "twoBit", or "2bit". Also note that in this case, the export method that is called is either the method with signature c("ANY", "character", "missing") or the method with signature c("ANY", "character", "character"), both defined in the BiocIO package. If object is a BSgenome object and the file extension or the format argument is "fasta", "twoBit", or "2bit", then the flow eventually reaches one of 2 methods documented here.
format	If not missing, should be "fasta", "twoBit", or "2bit" (case insensitive for "twoBit" and "2bit").
compress, compression_level	Forwarded to writeXStringSet. See ?writeXStringSet for the details.
verbose	Whether or not the function should display progress. TRUE by default.
...	Extra arguments. The method for TwoBitFile objects forwards them to bsapply.

Author(s)

Michael Lawrence

See Also

• BSgenome objects.

• The export generic function in the BiocIO package.

• FastaFile and TwoBitFile objects in the rtracklayer package.

Examples

library(BSgenome.Celegans.UCSC.ce2)
genome <- BSgenome.Celegans.UCSC.ce2

## Export as FASTA file.
out1_file <- file.path(tempdir(), "Celegans.fasta")
export(genome, out1_file)

## Export as twoBit file.
out2_file <- file.path(tempdir(), "Celegans.2bit")
export(genome, out2_file)

## Sanity checks:
dna0 <- DNAStringSet(as.list(genome))

system.time(dna1 <- import(out1_file))
stopifnot(identical(names(dna0), names(dna1)) && all(dna0 == dna1))

system.time(dna2 <- import(out2_file))  # importing twoBit is 10-20x
                                        # faster than importing non
                                        # compressed FASTA 
stopifnot(identical(names(dna0), names(dna2)) && all(dna0 == dna2))

Bioconductor/BSgenome documentation built on Oct. 31, 2024, 10:46 p.m.