Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes

Stable version, as published in the Journal of Open-Source Software.

Added

• pickle protocol implementation for Nodes, TrainingInfo, OrfFinder, Sequence, Masks and Genes objects.
• Buffer protocol implementation for Sequence, allowing access to raw digits.
• __eq__ and __repr__ magic methods to Mask objects.

Changed

• Optimized code used for region masking to avoid searching for the same mask repeatedly.
• TRANSLATION_TABLES and METAGENOMIC_BINS are now exposed as constants in the top pyrodigal module.
• Refactored connection scoring into different functions based on the type (start/stop) and strand (direct/reverse) of the node being scored.
• Changed the growth factor for dynamic arrays to be the same as the one used in CPython list buffers.