pyabricate 0.1.0

A Python port of ABRicate, a tool for mass screening of contigs for antibiotic resistance and virulence genes.

💊 PyABRicate

Pure Python port and interface to ABRicate, a tool for mass screening of contigs for antimicrobial resistance or virulence genes.

🗺️ Overview

ABRicate is a Perl command-line tool wrapping BLAST+ to perform screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB.

pyabricate is a pure-Python, batteries-included port of ABRicate, using the NCBI C++ Toolkit interface wrapped in pyncbitk to provide BLAST+ rather than using the BLAST+ binaries. It bundles the ABRIcate databases so that no additional data or dependencies are needed.

🔧 Installing

This project is supported on Python 3.7 and later.

PyABRicate can be installed directly from PyPI, which hosts some pure-Python wheels that also bundle the ABRicate databases.

$ pip install pyabricate

💡 Example

The command line of the original abricate script can be executed with a similar interface from a shell, and produces the same sort of table output:

$ pyabricate assembly.fa --mincov 50 --minid 50 --db ncbi
assembly.fa	LGJG01000041	35416	35844	-	fosB-251804940	1-429/429	===============	0/0	100.00	100.00	ncbi	NG_047889.1	FosB family fosfomycin resistance bacillithiol transferase
	FOSFOMYCIN
assembly.fa	LGJG01000040	190796	191281	+	dfrC	1-486/486	===============	0/0	100.00	99.59	ncbi	NG_047752.1	trimethoprim-resistant dihydrofolate reductase DfrC
	TRIMETHOPRIM
assembly.fa	LGJG01000038	62786	64543	-	blaR1	1-1758/1758	===============	0/0	100.00	92.83	ncbi	NG_047539.1	beta-lactam sensor/signal transducer BlaR1
	BETA-LACTAM
assembly.fa	LGJG01000038	64650	65495	+	blaZ	1-846/846	===============	0/0	100.00	96.81	ncbi	NG_055999.1	penicillin-hydrolyzing class A beta-lactamase BlaZ
	BETA-LACTAM
assembly.fa	LGJG01000038	62416	62796	-	blaI_of_Z	1-381/381	===============	0/0	100.00	95.28	ncbi	NG_047499.1	penicillinase repressor BlaI
	BETA-LACTAM

However, pyabricate also features an API which can be used to programmatically annotate any sequence:

import pyabricate

database = pyabricate.Database.from_name("ncbi")
abricate = pyabricate.ResistanceGeneFinder(database, min_coverage=50, min_identity=50)
sequence = "ATATTA..." # sequence in string format

for hit in abricate.find_genes(sequence):
    print(
        hit.gene.name, # resistance / virulence gene
        hit.alignment[0].start, # start coordinate in query sequence
        hit.alignment[0].stop,  # stop coordinate in query sequence
        hit.percent_coverage,
        hit.percent_identity
    )

The returned Hit objects contain all the information needed to build the table output in an object-oriented interface. ResistanceGeneFinder.find_genes accepts sequences as Python strings, which can be loaded with any other library such as Biopython.

💭 Feedback

⚠️ Issue Tracker

Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker if you need to report or ask something. If you are filing in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation.

🏗️ Contributing

Contributions are more than welcome! See CONTRIBUTING.md for more details.

📋 Changelog

This project adheres to Semantic Versioning and provides a changelog in the Keep a Changelog format.

⚖️ License

This library is provided under the GNU General Public License 3.0 or later. ABRicate was developed by Torsten Seemann and is redistributed under the terms of the GNU General Public License 2.0, see vendor/abricate/LICENSE.

This project is in no way not affiliated, sponsored, or otherwise endorsed by the original ABRIcate authors. It was developed by Martin Larralde during his PhD at the Leiden University Medical Center in the Zeller team.