Pyrodigal ¶

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Overview¶

Pyrodigal is a Python module that provides bindings to Prodigal using Cython. It directly interacts with the Prodigal internals, which has the following advantages:

single dependency: Pyrodigal is distributed as a Python package, so you can add it as a dependency to your project, and stop worrying about the Prodigal binary being present on the end-user machine.
no intermediate files: Everything happens in memory, in a Python object you fully control, so you don’t have to invoke the Prodigal CLI using a sub-process and temporary files. Sequences can be passed directly as strings or bytes, which avoids the overhead of formatting your input to FASTA for Prodigal.
lower memory usage: Pyrodigal is slightly more conservative when it comes to using memory, which can help process very large sequences. It also lets you save some more memory when running several meta-mode analyses
better performance: Pyrodigal uses SIMD instructions to compute which dynamic programming nodes can be ignored when scoring connections. This can save from a third to half the runtime depending on the sequence.

Setup¶

Run pip install pyrodigal 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 pyrodigal.

Library¶

License¶

This library is provided under the GNU General Public License v3.0. The Prodigal code was written by Doug Hyatt and is distributed under the terms of the GPLv3 as well. The cpu_features library was written by Guillaume Chatelet and is licensed under the terms of the Apache License 2.0.

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 European Molecular Biology Laboratory in the Zeller team.