seqinr: gbk2g2 – R documentation

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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 =  "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")

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

Biological Sequences Retrieval and Analysis

v4.2-16

GPL (>= 2)

Authors

Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]

Initial release

2022-05-19