Installation

alignparse requires Python 3.8 or higher and is currently tested on Python 3.11. A Mac OS X or Linux operating system is also required.

The easiest way to install alignparse is from PyPI using pip with:

pip install alignparse

Note that installing the dependency pysam may require additional packages on the host system. See the pysam documentation for more details.

In order to use the alignparse.minimap2 module, you need to install the minimap2 executable (version 2.17 or higher). You can do that via the bioconda recipe or from the program’s release page as described here.

An environment.yml file is provided with the source code. This can be used to create a conda environment that installs alignparse and its dependencies using:

conda env create -f environment.yml