Datasnakes-Scripts

The Datasnakes-Scripts package is a collection of the modules which aids in the analysis and visualization of orthologs-related bioinformatics projects.

Check out our wiki docs and our read the docs!

Installation

pip install Datasnakes-Scripts

Development Mode Installation

1. git clone http://github.com/datasnakes/Datasnakes-Scripts
2. cd Datasnakes-Scripts
3. pip install -e .

Manual Installation

Alternatively, you can set install the package manually.

1. Download the zip file and unzip it or git clone https://github.com/datasnakes/Datasnakes-Scripts.git
2. cd Datasnakes-Scripts
3. pip install .

Project Setup

This package is under development but still working. To test you'll want to create a virtual environment so that cleanup is easy. Using virtualenv with python3 insures that python invokes py3.5 and python3 invokes py36. Invoke python36.

$ mkdir dev
$ cd dev
$ virtualenv PackageTest --python=python3
$ source activate PackageTest
$ git clone http://github.com/datasnakes/Datasnakes-Scripts
$ cd Datasnakes-Scripts
$ python3 setup.py install or pip install .

Usage

After installation, you'll be able to easily import each module via:

from Datasnakes.Orthologs import Align, BioSQL, Blast, CompGenetics, Phylogenetics, Genbank

Tests

To run tests, type nosetests Tests/ in the Datasnakes-Orthologs directory.

Contributors

• Rob Gilmore | Github: @grabear | 📧
• Shaurita Hutchins | Github: @sdhutchins | Twitter: @MavenNBA | 📧

Citation

We're so thankful to have a resource such as Biopython. They inspired this package.

Cock, P.J.A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878

License

MIT