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

gbk2g2 {seqinr} | R Documentation

## 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

### 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)

[Package seqinr version 3.4-5 Index]