WriteGenes {DECIPHER}

R Documentation

Write Genes to a File

Description

Writes predicted genes to a file in GenBank (gbk) or general feature format (gff).

Usage

WriteGenes(x,
           file = "",
           format = "gbk",
           append = FALSE)

Arguments

x	An object of class Genes.
file	A connection or a character string naming the file path where the tree should be exported. If "" (the default), the tree is printed to the standard output connection, the console unless redirected by sink.
format	Character specifying "gbk" or "gff" output format.
append	Logical indicating whether to append to an existing file. Only applicable if file is a character string. If FALSE (the default), then the file is overwritten.

Details

WriteGenes will write a "Genes" object to a GenBank (if format is "gbk") or general feature format (if format is "gff") file.

Value

NULL.

Author(s)

Erik Wright eswright@pitt.edu

See Also

ExtractGenes, FindGenes, Genes-class

Examples

# import a test genome
fas <- system.file("extdata",
	"Chlamydia_trachomatis_NC_000117.fas.gz",
	package="DECIPHER")
genome <- readDNAStringSet(fas)

x <- FindGenes(genome)
WriteGenes(x[1:10,], format="gbk")
WriteGenes(x[1:10,], format="gff")

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