This release is a pre-release and may not be stable for production use.
lpbio
Scripts, tools and modules for computational biology
Scripts
When installed, the lpbio package provides the following scripts, available at the command-line:
bulk_prokka: for application ofprokkahttps://github.com/tseemann/prokka to a directory of input bacterial genome assemblies, taking advantage of local schedulers.
Modules
The lpbio package provides the following modules for use in Python applications and scripts
pysge: a module that writes job files compatible with SGE-like schedulers, and runs them.swarm: a module for interacting with theSwarmclustering tool and its output.
Development notes
Create a local environment, e.g. in conda, and install with pip install -e .:
$ conda create --name lpbio
$ source activate lpbio
$ pip install -e .
Tests
Tests are intended to be run with pytest from the repository root (using coverage and pytest-cov):
$ pwd
lpbio/
$ pytest --cov
1 maintainer
Metadata
1 maintainer
Release files for lpbio 0.1.0a0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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| lpbio-0.1.0a0.tar.gz | 12.8 kB | Without provenance | Details for lpbio-0.1.0a0.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| lpbio-0.1.0a0-py3-none-any.whl | Python 3 | none | any | Details for lpbio-0.1.0a0-py3-none-any.whl |
Total release size: 31.7 kB
Release files / lpbio-0.1.0a0.tar.gz
| Download URL | lpbio-0.1.0a0.tar.gz |
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| Size | 12.8 kB |
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Release files / lpbio-0.1.0a0-py3-none-any.whl
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| Tags | Python 3 |
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