genomics/bcftbx

Overview

genomics-bcftbx provides a Python library and a set of utilities used for NGS and genomics-related bioinformatics tasks, developed to support the Bioinformatics Core Facility (BCF) of the Faculty of Biology, Medicine and Health (FBMH) at the University of Manchester (UoM).

The bcftbx library provides submodules for various tasks, including:

• handling data from Illumina and SOLiD sequencing platforms;
• working with various file formats including Fastq, Fasta, MS Excel (.xls and .xlsx), HTML and tab-delimited (.tsv) files;
• running commands on local and cluster systems;
• general filesystem operations, text manipulation and checksumming.

The library includes a collection of utilities for tasks including:

• handling Illumina and SOLiD sequencing data;
• reporting outputs from bioinformatics software;
• analysing and reporting microarray data;
• performing basic manipulations on Fastq and Fasta files;
• working with MD5 checksumming of files.

Full documentation is available at http://genomics-bcftbx.readthedocs.org.

Installation

It is recommended to install the package into a Python virtualenv, for example:

virtualenv venv.bcftbx
. venv.bcftbx/bin/activate

To install a specific version, first download and unpack the source code, e.g.:

wget https://github.com/fls-bioinformatics-core/genomics/archive/2.0.0.tar.gz
tar zxf 2.0.0.tar.gz

Then install the package using:

pip install ./genomics-2.0.0

Note

It is also possible to use the package without installing it, by first ownloading and unpacking the .tar.gz archive and then adding the genomics directory to your PYTHONPATH environment and the bin directory to your PATH.

In this case you will also need to ensure that the additional packages required by the submodules are also installed (e.g. xlwt, xlrd and xlutils).

Documentation

Documentation based on sphinx is available under the docs directory.

To build do either:

python setup.py sphinx_build

or:

cd docs
make html

both of which create the documentation in the docs/build subdirectory.

Running Tests

The tests can be run using:

python setup.py test

In addition the tests are run by GitHub Actions whenever the repository is updated:

Developmental version

The developmental branch of the code on github is devel, this can be installed using:

pip install git+https://github.com/fls-bioinformatics-core/genomics.git@devel