diff --git a/CHANGELOG.md b/CHANGELOG.md index bba7e20..47e530d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,22 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unreleased] -[Unreleased]: https://github.com/althonos/pyrodigal/compare/v0.5.3...HEAD +[Unreleased]: https://github.com/althonos/pyrodigal/compare/v0.5.4...HEAD + + +## [v0.5.4] - 2021-09-18 +[v0.5.4]: https://github.com/althonos/pyrodigal/compare/v0.5.3...v0.5.4 + +### Added +- `Prediction.confidence` method to compute the confidence for a prediction like reported in Prodigal's GFF output. +- `Prediction.sequence` method get the nucleotide sequence of a predicted gene ([#4](https://github.com/althonos/pyrodigal/issues/4)). + +### Changed +- Replaced internal storage of input sequences to use a byte array instead of a bitmap. + +### Fixed +- Extract `Prediction.gc_cont` number directly from the start node instead of the text representation to get full accuracy. +- Prodigal bug causing nodes on the reverse strand to always receive a penalty instead of penalizing only small ORFs ([hyattpd/Prodigal#88](https://github.com/hyattpd/Prodigal/pull/88)). ## [v0.5.3] - 2021-09-12 diff --git a/pyrodigal/__init__.py b/pyrodigal/__init__.py index 53d254a..45e4c51 100644 --- a/pyrodigal/__init__.py +++ b/pyrodigal/__init__.py @@ -1,4 +1,7 @@ -from collections.abc import Sequence as _Sequence +from collections.abc import ( + Sequence as _Sequence, + Sized as _Sized, +) from . import _pyrodigal from ._pyrodigal import ( @@ -30,8 +33,9 @@ __author__ = "Martin Larralde " __license__ = "GPLv3" -__version__ = "0.5.3" +__version__ = "0.5.4" +_Sized.register(Sequence) _Sequence.register(Genes) _Sequence.register(Nodes) _Sequence.register(Predictions)