lpbio 0.1.0a0

Description:

lpbio 0.1.0a0

lpbio
Scripts, tools and modules for computational biology


Scripts
Modules
Development notes

Tests




Scripts
When installed, the lpbio package provides the following scripts, available at the command-line:

bulk_prokka: for application of prokka https://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 the Swarm clustering 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