seqinr (version 3.1-2)

gbk2g2: Conversion of a GenBank format file into a glimmer-like one

Description

This function reads a file in GenBank format and converts the features corresponding to CDS (Coding Sequences) into a format similar to glimmer program output.

Usage

gbk2g2(gbkfile =  "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.gbk",
g2.coord = "g2.coord")

Arguments

gbkfile

The name of the GenBank file

g2.coord

The name of the output file in glimmer-like format

Value

• The input file is returned invisibly.

Details

Partial CDS (either 5' or 3') and join in features are discarded.

References

citation("seqinr")

See Also

oriloc which uses glimmer-like files, gbk2g2.euk for eukaryotic sequences with introns.

Examples

# need internet connection
  	suppressWarnings(gbk2g2(g2.coord = "gbk2g2.test"))
  	res <- read.table("gbk2g2.test")
  	head(res)
  	stopifnot(nrow(res) == 892)