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Wub

Tools and software library developed by the Oxford Nanopore Technologies Applications group.

Features:

• Simple sequence and error simulation tools.
• Tools to visualise basic sequence properties.
• Fastq and fasta utilities.
• Tools to calculate read and genome assembly accuracy.
• Transcriptome alignment QC tools.
• Read couting and related utilities.
• BAM utilities.
• Miscellaneous utilities.

Getting Started

Installation

Set up a virtual environment

virtualenv  --system-site-packages wub_env
source wub_env/bin/activate
pip install --upgrade pip
pip install requests[security]

Then install the package via pip:

pip install git+https://github.com/nanoporetech/wub.git

If you installed the package in a virtual environment then do not forget to load it before using the package:

source wub_env/bin/activate

Run the following to leave the virtual environment:

deactivate

You can also clone the repository and install using setup.py:

git clone https://github.com/nanoporetech/wub.git
cd wub
python setup.py install

Install the package in developer mode:

python setup.py develop

Run the tests:

make test

Build the documentation:

make docs

Issue make help to get a list of make targets.

Documentation

Online documentation is avalaible at wub.readthedocs.io.

Contributing

• Please fork the repository and create a merge request to contribute.
• Please respect the structure outlined in scripts/_template_script.py from command line tools so documentation can be generated automatically.
• All non-trivial functions should have at least one test (with the exception of plotting functions).
• Use your best judgement when deciding whether to put a piece of code in a script or make it more reusable by incorporating it into the module.
• Use bumpversion to manage package versioning.
• The code should be PEP8 compliant, which can be tested by make lint.

Help

Licence and Copyright

(c) 2016 Oxford Nanopore Technologies Ltd.

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.