pybarrnap: Python implementation of barrnap

Table of contents

• Overview
• Installation
• CLI Usage
• API Usage
• LICENSE

Overview

pybarrnap is a python implementation of barrnap (Bacterial ribosomal RNA predictor). It provides a CLI compatible with barrnap and also provides a python API for running rRNA prediction and retrieving predicted rRNA. pybarrnap depends only on the python library and not on the external command-line tools nhmmer and bedtools.

Installation

Python 3.8 or later is required for installation. pybarrnap depends on pyhmmer and biopython.

Install PyPI package:

pip install pybarrnap

CLI Usage

Basic Command

pybarrnap genome.fna > genome_rrna.gff

Options

$ pybarrnap --help
usage: pybarrnap [options] genome.fna[.gz] > genome_rrna.gff

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

positional arguments:
  fasta              Input fasta file (or stdin)

optional arguments:
  -e , --evalue      E-value cutoff (default: 1e-06)
  -l , --lencutoff   Proportional length threshold to label as partial (default: 0.8)
  -r , --reject      Proportional length threshold to reject prediction (default: 0.25)
  -t , --threads     Number of threads (default: 1)
  -k , --kingdom     Target kingdom [bac|arc|euk|mito] (default: 'bac')
  -o , --outseq      Output rRNA hit seqs as fasta file (default: None)
  -i, --incseq       Include FASTA input sequences in GFF output (default: OFF)
  -q, --quiet        No print log on screen (default: OFF)
  -v, --version      Print version information
  -h, --help         Show this help message and exit

CLI Example

Click here to download examples dataset.

CLI Example 1

Print rRNA prediction result on screen

pybarrnap examples/bacteria.fna

CLI Example 2

Output rRNA predition result to file

pybarrnap examples/archaea.fna -k arc --outseq rrna.fna --incseq > rrna_incseq.gff

CLI Example 3

With pipe stdin

cat examples/mitochondria.fna | pybarrnap -q -k mito | grep 16S

API Usage

pybarrnap provides simple API for running rRNA prediction and retrieving predicted rRNA.

from pybarrnap import Barrnap
from pybarrnap.utils import load_example_fasta_file

# Get example fasta file path
fasta_file = load_example_fasta_file("bacteria.fna")

# Run pybarrnap rRNA prediction
barrnap = Barrnap(fasta_file, evalue=1e-6, lencutoff=0.8, reject=0.25, threads=1, kingdom="bac", quiet=False)
result = barrnap.run()

# Output rRNA GFF file
result.write_gff("bacteria_rrna.gff")
# Output rRNA GFF file (Include input fasta sequence)
result.write_gff("bacteria_rrna_incseq.gff", incseq=True)
# Output rRNA fasta file
result.write_fasta("bacteria_rrna.fna")

# Get rRNA GFF text and print
print("\n========== Print rRNA GFF ==========")
print(result.get_gff_text())

# Get rRNA features and print
print("\n========== Print rRNA features ==========")
for rec in result.seq_records:
    for feature in rec.features:
        print(feature.id, feature.type, feature.location, feature.qualifiers)

# Get rRNA sequences and print
print("\n========== Print rRNA sequences ==========")
for rec in result.get_rrna_seq_records():
    print(f">{rec.id}\n{rec.seq}")

LICENSE

pybarrnap uses Barrnap v0.9 HMM profile database created from Rfam and SILVA.

• pybarrnap: GPLv3
• Barrnap: GPLv3
• Rfam: CC0
• SILVA: Free for academic use