Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
GPL-3.0 License
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Published by github-actions[bot] 3 months ago
pyrodigal.cli
breaking the CLI.Published by github-actions[bot] 3 months ago
stdin
in CLI (#35).Pool
instead of ThreadPool
(#57).pyrodigal.cli.argument_parser
.pydata-sphinx-theme
.except *
statements in MetagenomicBins
.__init__
methods missing from all Cython types after the v3.0
update.Published by github-actions[bot] 5 months ago
Published by github-actions[bot] 5 months ago
strict
argument to Gene.translate
to control translation of ambiguous codons with unambiguous translation (#54).strict_translation
argument to Genes.write_genbank
and Genes.write_translation
.Gene.translate
.GeneFinder.train
.Genes.score
property to count the total score of all extracted genes.full_id
parameter to Genes.write_gff
, Genes.write_translation
and Genes.write_genes
to control the ID
field written for each gene (#53).Gene.translate
now raises a warning when called with a translation table incompatible with the training info.Published by github-actions[bot] 9 months ago
Scorer
internal API to separate connection scoring and overlap disentangling._shine_dalgarno_exact
and _shine_dalgarno_mm
methods of Sequence
.Nodes.__setstate__
caused by incorrect reallocation.Published by github-actions[bot] 11 months ago
pyrodigal.cli.main
.Published by github-actions[bot] 11 months ago
lz4
and xz
and zstd
-compressed input in the CLI.pyrodigal.cli.main
.Published by github-actions[bot] about 1 year ago
min_mask
argument to GeneFinder
to control the minimum lenght of masked regions on mask=True
.Published by github-actions[bot] about 1 year ago
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.TrainingInfo
properties (missing_motif_weight
, coding_statistics
).TrainingInfo
properties.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%.Genes.write_gff
not properly reporting the number of bytes written.nogil
sections in Sequence
constructor.noexcept
qualifier.OrfFinder
to GeneFinder
for consistency.memoryview
to expose all TrainingInfo
attributes instead manually building lists or tuples.pyrodigal.lib
) to allow importing the underlying classes in other Cython projects.typing.Literal
for allowed translation table values in pyrodigal.lib
annotationsNodes._raw_coding_score
to reduce calls to pow
and log
functions.struct _node
fields to reduce size in memory.GeneFinder.find_genes
and GeneFinder.train
reserve memory for the Nodes
based on the GC% of the input sequence.ConnectionScorer.compute_skippable
.freelist
for allocating Node
, Gene
, MetagenomicBin
and Mask
.Genes
and Nodes
to reduce early reallocations.metagenomic_bin
attribute of TrainingInfo
.Published by github-actions[bot] about 1 year ago
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%.Nodes._raw_coding_score
to reduce calls to pow
and log
functions.struct _node
fields to reduce size in memory.GeneFinder.find_genes
and GeneFinder.train
reserve memory for the Nodes
based on the GC% of the input sequence.ConnectionScorer.compute_skippable
.Published by github-actions[bot] about 1 year ago
nogil
sections in Sequence
constructor.noexcept
qualifier.freelist
for allocating Node
, Gene
, MetagenomicBin
and Mask
.Genes
and Nodes
to reduce early reallocations.Published by github-actions[bot] about 1 year ago
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.Genes.write_gff
not properly reporting the number of bytes written.typing.Literal
for allowed translation table values in pyrodigal.lib
annotationsPublished by github-actions[bot] about 1 year ago
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.TrainingInfo
properties (missing_motif_weight
, coding_statistics
).TrainingInfo
properties.TrainingInfo
constructor with configuration option for all attributes.TrainingInfo.to_dict
method to extract all parameters from a TrainingInfo
.OrfFinder
to GeneFinder
for consistency.pyrodigal.lib
) to allow importing the underlying classes in other Cython projects.memoryview
to expose all TrainingInfo
attributes instead manually building lists or tuples.metagenomic_bin
attribute of TrainingInfo
.Published by github-actions[bot] over 1 year ago
v3.0.0
.Published by github-actions[bot] over 1 year ago
Sequence.__init__
.archspec
instead of cpu_features
for runtime feature detection.Published by github-actions[bot] over 1 year ago
v2.6.3+c1e2d36
to fix a bug with Shine-Dalgarno detection on reverse contig edge (hyattpd/Prodigal#100).