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Common code shared among in-house Bioinformatics python packages

Project description

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

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
bbcu.bioutils-1.0.4.tar.gz (14.0 kB) Copy SHA256 hash SHA256 Source None Jun 27, 2018

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