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@github-actions github-actions released this 17 Sep 14:32
v3.0.0
e3b8350

Added

  • MetagenomicBins collection to store a dense array of MetagenomicBin objects.
  • metagenomic_bins keyword argument to GeneFinder allowing to control which models are used when running gene finding in meta mode (#24).
  • metagenomic_bin attribute to Genes referencing the metagenomic model with which the genes were predicted, if in meta mode.
  • Additional TrainingInfo properties (missing_motif_weight, coding_statistics).
  • Setters for all remaining TrainingInfo properties.
  • Proper TrainingInfo constructor with configuration option for all attributes.
  • TrainingInfo.to_dict method to extract all parameters from a TrainingInfo.
  • Genes.write_genbank method to write a GenBank record with all predicted genes from a sequence.
  • include_stop flag to Gene.translate and Genes.write_translations to allow excluding the stop codon from the translated sequence.
  • include_translation_table flag to Genes.write_gff to include the translation table to the GFF attributes of each gene.
  • gbk output format to the Pyrodigal CLI.
  • Sequence.unknown property exposing the number of unknown nucleotides in the sequence.
  • Sequence.start_probability and Sequence.stop_probability to estimate the probability of encountering a start and a stop codon based on the GC%.

Fixed

  • Genes.write_gff not properly reporting the number of bytes written.
  • Merge several nogil sections in Sequence constructor.
  • Several Cython functions missing a noexcept qualifier.

Changed

  • BREAKING: Rename OrfFinder to GeneFinder for consistency.
  • BREAKING: Use memoryview to expose all TrainingInfo attributes instead manually building lists or tuples.
  • Reorganize memory management of the built-in metagenomic models.
  • Make the internal Cython model public (pyrodigal.lib) to allow importing the underlying classes in other Cython projects.
  • Use typing.Literal for allowed translation table values in pyrodigal.lib annotations
  • Cache intermediate log-odds in Nodes._raw_coding_score to reduce calls to pow and log functions.
  • Inline connection scoring functions to reduce function call overhead.
  • Reorganize struct _node fields to reduce size in memory.
  • Make GeneFinder.find_genes and GeneFinder.train reserve memory for the Nodes based on the GC% of the input sequence.
  • Avoid storing temporary results in the generic implementation of ConnectionScorer.compute_skippable.
  • Use Cython freelist for allocating Node, Gene, MetagenomicBin and Mask.
  • Increase minimum allocation for Genes and Nodes to reduce early reallocations.

Removed

  • BREAKING: metagenomic_bin attribute of TrainingInfo.
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