PyCoMSA 
#
Cython bindings and Python interface to CoMSA, a compressor for multiple sequence alignments.
Overview#
PyCoMSA is a Python module that provides bindings to Prodigal using Cython. It directly interacts with the CoMSA internals, which has the following advantages:
Just add pycomsa as a pip or conda dependency, no need
for the CoMSA binary or any external dependency.
Build alignments to compress as Python str or byte-like objects, no
need for intermediate files.
Pick the file format based on your needs, and not based on the file format of the original aligmnment.
Support reading and writing files for any architecture, and not just native one as the original CoMSA.
Load files generated with PyCoMSA using CoMSA, as both are using the same compression method.
Access all the features of the original CLI through the Python API.
Setup#
Run pip install pycomsa in a shell to download the latest release and all
its dependencies from PyPi, or have a look at the
Installation page to find other ways to install
pycomsa.
Library#
Check the following pages of the user guide or the API reference for more in-depth reference about library setup, usage, and rationale:
License#
This library is provided under the GNU General Public License v3.0. The Prodigal code was written by Sebastian Deorowicz and is distributed under the terms of the GPLv3 as well. See the Copyright Notice section for the full GPLv3 license.
This project is in no way not affiliated, sponsored, or otherwise endorsed by the original `Prodigal`_ authors. It was developed by Martin Larralde during his PhD project at the Leiden University Medical Center in the Zeller team.