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, ...)
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 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 writeXStringSet (export)
or the readDNAStringSet 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
writeXStringSet (export) and the
readDNAStringSet family of functions
(import).
See export-methods in the BSgenome package for
exporting a BSgenome object as a FASTA file.