read.gff: Read a GFF file from NCBI

In cstubben/genomes2: Genome sequencing project metadata

Description

Read a GFF file from NCBI genomes ftp (version 3)

Usage

read.gff(file,  locus.tags = TRUE, nrows = -1) 

Arguments

file	a GFF file
locus.tags	only return genes with locus tags
nrows	number of rows to read

Details

GFF files are available from the NCBI genomes ftp directory, ftp://ftp.ncbi.nih.gov/genomes.

Value

GRanges with 4 elementMetadata columns: locus, feature, description and gene name. If all rows are returned (locus.tags=FALSE), then score, phase and tags are included. The seqid and source are saved in metadata.

Note

By default, the GFF file is parsed to return only features with locus_tag keys. Gene types, products and names are assigned from child records by matching Parent tags.

The function is intended to load GFF files from NCBI only. GFF files from other sources have not been tested and may not parse.

Author(s)

Chris Stubben

References

see http://www.sequenceontology.org/gff3.shtml for details about Generic Feature Format

See Also

read.ncbi.ftp

Examples

 file<-"ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Yersinia_pestis_CO92_uid57621/NC_003132.gff"
 x <-read.gff(file)
 x
metadata(x)
 

cstubben/genomes2 documentation built on May 14, 2019, 12:25 p.m.