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Cortexpy is a Python package for sequence analysis using linked and colored De Bruijn graphs such as the ones created by Cortex and Mccortex. This project aims to mirror many of the features contained in CortexJDK.
Cortexpy also comes with a command-line tool for basic inspection and manipulation of Cortex graphs with and without links.
Audience
The audience of cortexpy is researchers working with colored De Bruijn graphs and link information in Cortex and Mccortex format.
Free software
Cortexpy is free software; you can redistribute it and/or modify it under the terms of the Apache License version 2.0. Contributions are welcome. Please join us on GitHub.
Installation
pip install cortexpy
Documentation
For more information, please see cortexpy documentation.
Citing cortexpy
If you use cortexpy in your work, please consider citing:
Akhter, Shirin, Warren W. Kretzschmar, Veronika Nordal, Nicolas Delhomme, Nathaniel R. Street, Ove Nilsson, Olof Emanuelsson, and Jens F. Sundström. “Integrative analysis of three RNA sequencing methods identifies mutually exclusive exons of MADS-box isoforms during early bud development in Picea abies.” Frontiers in Plant Science 9 (2018). https://doi.org/10.3389/fpls.2018.01625
Bugs
This code is maintained by Warren Kretzschmar <winni@warrenwk.com>. For bugs, please raise a GitHub issue.
Development
Install conda.
Download mccortex for testing:
conda env create -f environment.yml -n my-dev-environment
Activate development environment:
conda activate my-dev-environment
Install remaining development tools:
pip3 install -r requirements.txt
All remaining commands in the development section need to be run in an activated conda dev environment.
Tests
make test
Deploy new cortexpy version to pypi
Requires access credentials for pypi.
make deploy
Building the docs
The documentation is automatically built by read-the-docs on push to master. To build the documentation manually:
# install sphinx dependencies pip install -r docs/requirements.txt make docs
1 maintainer
Release files for cortexpy 0.46.5
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| cortexpy-0.46.5.tar.gz | 212.1 kB | Details |
Release files / cortexpy-0.46.5.tar.gz
| Download URL | cortexpy-0.46.5.tar.gz |
|---|---|
| Size | 212.1 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/40.6.2 requests-toolbelt/0.9.1 tqdm/4.42.1 CPython/3.7.2
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