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pymummer
========
Python3 wrapper for running MUMmer and parsing the output.
[](https://travis-ci.org/sanger-pathogens/pymummer)
Installation
------------
###Homebrew/LinuxBrew###
```
brew tap homebrew/python
brew install pymummer
```
##Pip
###Pre-requisites###
The MUMmer package must be installed.
Instructions to install MUMmer can be found [here](http://mummer.sourceforge.net/manual/#installation)
###Installation###
Install with
pip3 install pymummer
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 promer class###
[TODO]
###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
Contact
-------
Authors: Martin Hunt, Nishadi De Silva
Affiliation: Wellcome Trust Sanger Institute, Hinxton, UK
Email: path-help@sanger.ac.uk
|
