barrnap: Finding rRNA genes

Description

Locating all rRNA genes in genomic DNA using the barrnap software.

Usage

barrnap(genome.file, bacteria = TRUE, cpu = 1)

Arguments

genome.file

A fasta-formatted file with the genome sequence(s).

bacteria

Logical, the genome is either a bacteria (default) or an archea.

cpu

Number of CPUs to use, default is 1.

Value

A gff.table (see readGFF for details) with one row for each detected rRNA sequence.

Details

The external software barrnap is used to scan through a prokaryotic genome to detect the rRNA genes (5S, 16S, 23S). This free software can be installed from https://github.com/tseemann/barrnap.

Examples

Run this code

# NOT RUN {
# This example requires the external barrnap software
# Using a genome file in this package.
xpth <- file.path(path.package("micropan"),"extdata")
genome.file <- file.path(xpth,"Example_genome.fasta.xz")

# We need to uncompress it first...
tf <- tempfile(fileext=".xz")
s <- file.copy(genome.file,tf)
tf <- xzuncompress(tf)

# Searching for rRNA sequences, and inspecting
gff.table <- barrnap(tf)
print(gff.table)

# Retrieving the sequences
genome <- readFasta(tf)
rRNA.fasta <- gff2fasta(gff.table,genome)

# ...and cleaning...
file.remove(tf)
# }
# NOT RUN {
# }