pyrodigal

Fixed

• Some cpu_features source files not being included in source distribution.

Added

• load and dump methods to TrainingInfo for storing and loading a raw training info structure.
• Support for creating an OrfFinder pre-configured with a training info.
• -t and -n flags to the CLI.

Added

• pyrodigal command line script exposing a CLI mimicking the original prodigal binary.
• write_gff, write_genes and write_translations methods to pyrodigal.Predictions to write the predictions results to a file in different formats.
• Implementation for masking regions of unknown nucleotides in input sequences.

Changed

• Renamed pyrodigal.Pyrodigal class to pyrodigal.OrfFinder.

Fixed

• setup.py build different SIMD implementations with the same set of feature flags, causing compilers to re-optimize the SIMD implementations.

Added

• Sphinx documentation with small install guide and API reference.

Fixed

• setup.py not detecting SSE2 and AVX2 build support because of a linker error.

Changed

• Build OSX extension without AVX2 support since runtime detection of AVX2 to avoid the Illegal Instruction: 4 bug on older CPUs.

Fixed

• Source distribution lacking C files necessary for building cpu_features.

Added

• SIMD code to build an index of which connections can be skipped when scoring node connections in the dynamic programming routine (#6).

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).

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).

Fixed

• Prediction.translate not translating the last unknown codon properly for genes on the direct strand.

Changed

• Make Pyrodigal.train return a reference to the newly created TrainingInfo for inspection if needed.
• Reimplement add_nodes and add_genes to use a growable array instead of counting and pre-allocating the C arrays.

Fixed

• Inconsistent handling of unknown nucleotides in input sequences and gene translations.

Added

• Additional Gene properties to access the score

Changed

• Use more efficient PyUnicode macros when reading or creating a string containing a nucleotide or a protein sequence.
• Release the GIL when creating a bitmap for an str given as input to Pyrodigal.find_genes.
• Release the GIL when creating the protein sequence returned by Gene.translate.

Fixed

• Pyrodigal.find_genes and Gene.translate not behaving like Prodigal when handling sequences with unknown nucleotides.

Added

• pyrodigal.TrainingInfo class exposing variables obtained during training as an attribute to Pyrodigal, Gene and Genes instance.
• Support for passing objects implementing the buffer protocol to Pyrodigal.find_genes and Pyrodigal.train instead of requiring str sequences.

Fixed

• Potential data race on training info in case a Gene.translate with a non-default translation table was being translated at the same time as a Pyrodigal.find_genes call.
• Spurious handling of Unicode strings causing potential issues on platform using a different base encoding.

Fixed

• Pyrodigal.find_genes segfaulting on some sequences when called in single mode (#2).
• MemoryError potentially not being properly raised on allocation issues for sequence bitmaps.

Changed

• Tests are now in the pyrodigal.tests module and can be run after a site install.

Fixed

• Pyrodigal.find_genes stalling on sequences shorter than 3 nucleotides.

Fixed

• Compilation of OSX and Windows wheels.

Fixed

• Mark package as OS-independent.

Added

• Support for Python 3.5.
• Compilation of PyPy wheels on OSX.

Fixed

• Buffer overflow when running in meta mode on a sequence too small to have any dynamic programming nodes.

Fixed

• Buffer overflow coming from the node array, caused by an incorrect
  estimation of the node count from the sequence length.

Removed

• Python 3.5 from the project metadata (the code was only compatible with
  Python 3.6+ already because of f-strings).

Fixed

• Broken linking of static libprodigal against the _pyrodigal extension
  on some OSX environments (bioconda/bioconda-recipes#25568).

Changed

• trans_table keyword argument to Pyrodigal.train has been renamed
  to translation_table.

Added

• Option to change the translation table to any allowed number in Gene.translate
  (#1).

Fixed

• Broken compilation of PyPy wheels in Travis-CI.