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

In seqinr: Biological Sequences Retrieval and Analysis

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 =  "https://pbil.univ-lyon1.fr/datasets/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

Details

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

Value

The input file is returned invisibly.

Author(s)

J.R. Lobry

References

citation("seqinr")

See Also

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

Examples

  ## Not run:  # need internet connection
  	suppressWarnings(gbk2g2(g2.coord = "gbk2g2.test"))
  	res <- read.table("gbk2g2.test")
  	head(res)
  	stopifnot(nrow(res) == 892)
  
## End(Not run)

seqinr documentation built on May 29, 2024, 6:36 a.m.