write.FeatureTable-methods: Write GenBank records or features to file in Feature Table...

In biofiles: An Interface for GenBank/GenPept Flat Files

Description

Feature Tables are simple five-column tab-delimited tables specifying the location and type of each feature. They can be used as input for tbl2asn or Sequin to generate annotation.

Usage

write.FeatureTable(x, file, tablename = "", dbname = "", sequence = FALSE,
  append = FALSE, ...)

## S4 method for signature 'gbRecord'
write.FeatureTable(x, file, tablename = "",
  dbname = "", sequence = FALSE, append = FALSE)

## S4 method for signature 'gbFeatureTable'
write.FeatureTable(x, file, tablename = "",
  dbname = "", sequence = FALSE, append = FALSE)

Arguments

x	A gbRecord instance.
file	A connection or a character string naming the file to write to.
tablename	Optional table name to appear in the first line of the feature table.
dbname	Data base name associated with the CDS qualifier protein_id.
sequence	if TRUE, additionally output a fasta file.
append	if TRUE the data is appended to the connection.
...	Additional arguments passed to methods.

Examples

## Not run: 
load(system.file("extdata", "marine_metagenome.rda", package = "biofiles"))
write.FeatureTable(x, file = "data/marine_metagenome.tbl")

## End(Not run)

biofiles documentation built on May 2, 2019, 3:31 p.m.