FastaFile-class {rtracklayer}R Documentation

FastaFile objects

Description

These functions support the import and export of the Fasta sequence format, using the Biostrings package.

Usage

## S4 method for signature 'FastaFile,ANY,ANY'
import(con, format, text,
           type = c("DNA", "RNA", "AA", "B"), ...)

## S4 method for signature 'ANY,FastaFile,ANY'
export(object, con, format, ...)
## S4 method for signature 'XStringSet,FastaFile,ANY'
export(object, con, format, ...)
## S4 method for signature 'BSgenome,FastaFile,ANY'
export(object, con, format, ...)

Arguments

con

A path or FastaFile object. URLs and connections are not supported. If con is not a FastaFile, either the file extension or the format argument needs to be “fasta”. Compressed files (“gz”, “bz2” and “xz”) are handled transparently.

object

The object to export, should be an XStringSet, BSgenome or something coercible to a DNAStringSet, like a character vector.

format

If not missing, should be “fasta”.

text

If con is missing, a character vector to use as the input

type

Type of biological sequence.

...

Arguments to pass down to write.XStringSet (export) or the read.DNAStringSet family of functions (import).

FastaFile objects

The FastaFile class extends RTLFile and is a formal represention of a resource in the Fasta format. To cast a path, URL or connection to a FastaFile, pass it to the FastaFile constructor.

Author(s)

Michael Lawrence

See Also

These functions are implemented by the Biostrings write.XStringSet (export) and the read.DNAStringSet family of functions (import).


[Package rtracklayer version 1.20.0 Index]