Releases: althonos/pyrodigal
Releases · althonos/pyrodigal
v3.4.1
v3.4.0
Added
strict
argument toGene.translate
to control translation of ambiguous codons with unambiguous translation (#54).strict_translation
argument toGenes.write_genbank
andGenes.write_translation
.- Support for translation tables 26 to 33 in
Gene.translate
. - Support for translation tables 26, 29, 30, 32 and 33 in
GeneFinder.train
. Genes.score
property to count the total score of all extracted genes.full_id
parameter toGenes.write_gff
,Genes.write_translation
andGenes.write_genes
to control theID
field written for each gene (#53).
Changed
Gene.translate
now raises a warning when called with a translation table incompatible with the training info.
Fixed
- Bug in code for masking trailing nucleotides (#55).
v3.3.0
Added
Changed
Scorer
internal API to separate connection scoring and overlap disentangling.
Fixed
- Bug with computation of minimum node in connection scoring loop (hyattpd/Prodigal#108).
- Out-of-bounds sequence access in
_shine_dalgarno_exact
and_shine_dalgarno_mm
methods ofSequence
. - Memory leak in
Nodes.__setstate__
caused by incorrect reallocation.
v3.2.2
v3.2.1
Added
- Option to change argument parser in
pyrodigal.cli.main
.
v3.2.0
Added
- AVX-512 implementation of the SIMD pre-filter.
- Additional support for reading
lz4
andxz
andzstd
-compressed input in the CLI. - Option to change gene finder type in
pyrodigal.cli.main
.
v3.1.1
v3.1.0
Added
- Support for Python 3.12.
min_mask
argument toGeneFinder
to control the minimum lenght of masked regions onmask=True
.
v3.0.1
v3.0.0
Added
MetagenomicBins
collection to store a dense array ofMetagenomicBin
objects.metagenomic_bins
keyword argument toGeneFinder
allowing to control which models are used when running gene finding in meta mode (#24).metagenomic_bin
attribute toGenes
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 aTrainingInfo
.Genes.write_genbank
method to write a GenBank record with all predicted genes from a sequence.include_stop
flag toGene.translate
andGenes.write_translations
to allow excluding the stop codon from the translated sequence.include_translation_table
flag toGenes.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
andSequence.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 inSequence
constructor. - Several Cython functions missing a
noexcept
qualifier.
Changed
- BREAKING: Rename
OrfFinder
toGeneFinder
for consistency. - BREAKING: Use
memoryview
to expose allTrainingInfo
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 inpyrodigal.lib
annotations - Cache intermediate log-odds in
Nodes._raw_coding_score
to reduce calls topow
andlog
functions. - Inline connection scoring functions to reduce function call overhead.
- Reorganize
struct _node
fields to reduce size in memory. - Make
GeneFinder.find_genes
andGeneFinder.train
reserve memory for theNodes
based on the GC% of the input sequence. - Avoid storing temporary results in the generic implementation of
ConnectionScorer.compute_skippable
. - Use Cython
freelist
for allocatingNode
,Gene
,MetagenomicBin
andMask
. - Increase minimum allocation for
Genes
andNodes
to reduce early reallocations.
Removed
- BREAKING:
metagenomic_bin
attribute ofTrainingInfo
.