pymummer
Python3 wrapper for running MUMmer and parsing the output.
Contents
Introduction
Runs MUMmer and parses the output.
Installation
pymummer has the following dependencies:
Required dependencies
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
Using pip
pip3 install pymummer
Running the tests
The test can be run from the top level directory:
python setup.py test
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.