lpbio

Scripts, tools and modules for computational biology

• lpbio
  • 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 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 (coverage can be measured using coverage and pytest-cov):

$ pwd
lpbio/
$ pytest --cov