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

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/gbk2g2.euk.R

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. This function is specifically made for eukaryotic sequences, i.e. with introns.

Usage

1
2
gbk2g2.euk(gbkfile = system.file("sequences/ame1.gbk", package ="seqinr"),
g2.coord = "g2.coord")

Arguments

gbkfile

The name of the GenBank file

g2.coord

The name of the output file

Details

This function returns the coordinates of the exons annotated in the GenBank format file.

Value

A data frame with three columns will be written to the g2.coord file. The first column corresponds to the name of the gene, given in the GenBank file through the /gene feature. The second and third column contain the start and the stop position of the exon.

Author(s)

J.R. Lobry, A. Nec<c5><9f>ulea

References

citation("seqinr")

See Also

oriloc, gbk2g2

Examples

1
 ## Not run:  gbk2g2.euk() 

seqinr documentation built on May 30, 2017, 12:54 a.m.

Search within the seqinr package
Search all R packages, documentation and source code