pymummer

Python3 wrapper for running MUMmer and parsing the output.

Contents

• Introduction
• Installation
  • Required dependencies
  • Homebrew/LinuxBrew
  • Using pip
  • Running the tests
• Usage (for developers)
  • pymummer nucmer class
  • pymummer coords_file class
  • pymummer alignment class
• License
• Feedback/Issues

Introduction

Runs MUMmer and parses the output.

Installation

pymummer has the following dependencies:

Required dependencies

• MUMmer

There are a number of ways to install pymummer and details are provided below. If you encounter an issue when installing pymummer please contact your local system administrator. If you encounter a bug please log it here or email us at path-help@sanger.ac.uk.

Homebrew/LinuxBrew

brew tap homebrew/python
brew install pymummer

Conda

We have provided conda environment recipes in this repo that can be used to create a fresh environment with the required dependencies. After creating a new env you can pip install pymummer from pypi or this repo using the commands in the next section.

# Create pymummer env 
conda env create -f environment.yml
# Activate env
conda activate pymummer
# Install pymummer
pip install pymummer

If you are using an M-Series Mac (ARM64 processor) you will need to create a mock Intel environment to install Mummer4 from Bioconda.

# Apple ARM64 Macs only
# Create mock Intel env
conda env create -f env_osx64.yml
# Activate env
conda activate pymummer-osx64
# Install pymummer
pip install pymummer

Pip install

Install from PyPi

pip3 install pymummer

Or pip install the latest development version directly from this repo.

pip3 install git+https://github.com/sanger-pathogens/pymummer.git

Running the tests

The test can be run from the top level directory:

pytest tests

Usage (for developers)

Example showing how pymummer can be used to run nucmer on a fasta file and parse the output file to produce a set of alignment objects:

from pymummer import coords_file, alignment, nucmer
...
runner = nucmer.Runner(reference_file, query_file, results_file) 
runner.run()
file_reader = coords_file.reader(results_file)
alignments = [coord for coord in file_reader if not coord.is_self_hit()] #Remove self hits
...

pymummer nucmer class

Wraps the nucmer, delta-filter, show-coords and show-snps commands.

Arguments:

__ref__			reference file  
__query__			query file  
__outfile__		output file  
__min\_id__		min\_id for delta-filter command (default None)  
__min\_length__	min\_length for delta-filter command (default None)  
__breaklen__		breaklen for nucmer command (nucmer's default is 200)   
__coords\_header__	print header in show-coords output (default True)  
__maxmatch__		maxmatch for nucmer (default False)  
__show\_snps__		run show-snps (default False)  
__snps\_header__ 	print header in show-snps output (default True)  

pymummer coords_file class

Parses the nucmer output and populate an alignment object for each hit in the output

pymummer alignment class

Check attributes of a hit, swap the reference and query, check if it's a self hit and so on

License

pymummer is free software, licensed under GPLv3.

Feedback/Issues

Please report any issues to the issues page or email path-help@sanger.ac.uk.