CONDOP (version 1.0)

read.annot.from.gff: Read a GFF file from NCBI and return a GRanges object.

Description

Read a GFF file from NCBI and return a GRanges object.

Usage

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

Arguments

gff.file

a GFF file

locus.tags

only return genes with locus tags. Defaults to TRUE.

nrows

number of rows to read.

verbose

Indicate whether information about the process should be reported. Defaults to TRUE.

Value

GRanges with 4 elementMetadata columns: locus, proetin id, gene id, feature, description and gene name. If all rows are returned (locus.tags=FALSE), then score, phase and tags are included.