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, ...)

### 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.

[Package rtracklayer version 1.46.0 Index]