pymummer
Python3 module for running MUMmer and reading the output
Science Score: 10.0%
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○codemeta.json file
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✓Committers with academic emails
4 of 7 committers (57.1%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (15.7%) to scientific vocabulary
Keywords from Contributors
Repository
Python3 module for running MUMmer and reading the output
Basic Info
- Host: GitHub
- Owner: sanger-pathogens
- License: other
- Language: Python
- Default Branch: master
- Size: 107 KB
Statistics
- Stars: 33
- Watchers: 12
- Forks: 10
- Open Issues: 4
- Releases: 0
Metadata Files
README.md
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
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.
```bash
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.
```bash
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
bash
pip3 install pymummer
Or pip install the latest development version directly from this repo.
bash
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.
Owner
- Name: Pathogen Informatics, Wellcome Sanger Institute
- Login: sanger-pathogens
- Kind: organization
- Location: Hinxton, Cambs., UK
- Website: http://www.sanger.ac.uk/science/groups/pathogen-informatics
- Repositories: 54
- Profile: https://github.com/sanger-pathogens
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 3
- Watch event: 7
- Issue comment event: 11
- Member event: 2
- Push event: 2
- Pull request event: 3
Last Year
- Create event: 1
- Release event: 1
- Issues event: 3
- Watch event: 7
- Issue comment event: 11
- Member event: 2
- Push event: 2
- Pull request event: 3
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| martinghunt | m****t@g****m | 37 |
| Martin Hunt | m****2@s****k | 18 |
| Ben Taylor | b****r@s****k | 5 |
| nds | n****s@s****k | 5 |
| Sara Sjunnebo | s****4@s****k | 3 |
| andrewjpage | a****e@g****m | 2 |
| Adam Taranto | a****o@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 7
- Total pull requests: 34
- Average time to close issues: over 1 year
- Average time to close pull requests: 27 days
- Total issue authors: 6
- Total pull request authors: 7
- Average comments per issue: 1.86
- Average comments per pull request: 0.24
- Merged pull requests: 33
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 1
- Average time to close issues: about 22 hours
- Average time to close pull requests: about 12 hours
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 2.0
- Average comments per pull request: 4.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Adamtaranto (2)
- wlh1234 (1)
- notestaff (1)
- mthang (1)
- zmunro (1)
Pull Request Authors
- martinghunt (22)
- nds (4)
- ssjunnebo (3)
- Adamtaranto (3)
- rpetit3 (2)
- bewt85 (1)
- nagesh4193 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 1,054 last-month
- Total docker downloads: 6,888
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 17
(may contain duplicates) - Total versions: 27
- Total maintainers: 3
pypi.org: pymummer
Wrapper for MUMmer
- Documentation: https://pymummer.readthedocs.io/
- License: GPLv3
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Latest release: 0.12.0
published over 1 year ago
Rankings
Maintainers (2)
spack.io: py-pymummer
Python3 module for running MUMmer and reading the output
- Homepage: https://github.com/sanger-pathogens/pymummer
- License: []
-
Latest release: 0.11.0
published over 2 years ago
Rankings
Maintainers (1)
Dependencies
- pyfastaq *