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A python library for comparative genomics of microbial "islands"
Clone the repository and install with pip:
pip install -e .
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├── README.md <- The top-level README for developers using this project.
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├── docs <- *TBD* A default Sphinx project; see sphinx-doc.org for details
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│── bin <- Miscellaneous standalone scripts
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├── requirements.txt <- The requirements file for building the libary
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├── setup.py <- makes project pip installable
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├── pyIsland <- Source code for use in this project.
│ ├── __init__.py <- Makes pyIsland a Python module
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│ ├── Drivers <- Python wrappers around cmd line programs
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│ ├── GCP <- Convenience fxns for working with GCP
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│ ├── Parsers <- Common parsers
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│ ├── FastaUtils <- Wrappers around BioPython for fasta manipulation
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│ ├── Islands <- Extracting genomic regions and annotating them
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│ ├── tests <- Unit tests with pytest
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│ ├── TBD <- TBD
TBD
This project comes with pytest and black. Run pytest using
pytest pyIsland/tests/ --cov=pyIsland
And format the code using
black pyIsland/