bbcu.bioutils 1.0.4

Common code shared among in-house Bioinformatics python packages

Desctiption

Common code shared among in-house Bioinformatics python packages, such as:

• Parsing of FastQC output

• Manipulating FASTA sequences

• Building and using database of conversion GeneBank id (gi) to scientific name

Python version

This project is currently using Python 2.7

Installation

It is recommended to use virtualenv to create a clean python environment.

To install bioutils, use pip:

pip install bbcu.bioutils

Testing

To run unit tests, use:

nosetests

Or:

tox

This suite includes both unit and more time-consuming integration tests

Execution

The main script shipped with this project is gi2name.py, see its options by running:

The database is built by the script: build-taxonomy-db.py