Metadata-Version: 2.1
Name: lpbio
Version: 0.1.0a0
Summary: lpbio provides scripts and modules for computational biology
Home-page: http://widdowquinn.github.io/lpbio/
Author: Leighton Pritchard
Author-email: leighton.pritchard@hutton.ac.uk
License: MIT
Download-URL: https://github.com/widdowquinn/lpbio/releases
Keywords: genome bioinformatics sequence
Platform: Posix; MacOS X
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown

# `lpbio`

Scripts, tools and modules for computational biology

<!-- TOC -->

- [Scripts](#scripts)
- [Modules](#modules)
- [Development notes](#development-notes)
    - [Tests](#tests)

<!-- /TOC -->

## 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](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`](https://github.com/torognes/swarm) clustering tool and its output.

## Development notes

Create a local environment, e.g. in `conda`, and install with `pip install -e .`:

```bash
$ 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`):

```bash
$ pwd
lpbio/
$ pytest --cov
```

