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] almost 2 years ago
Published by github-actions[bot] almost 2 years ago
Published by github-actions[bot] almost 2 years ago
Sequence.gc_frame_plot
method to compute the max GC frame profile from Python.metagenomic_bin
property to TrainingInfo
to support recovering the object corresponding to a pre-trained model.meta
attribute to Genes
to store whether genes were predicted in single or in meta mode.pyrodigal.PRODIGAL_VERSION
constant storing the wrapped Prodigal version.pyrodigal.MIN_SINGLE_GENOME
and pyrodigal.IDEAL_SINGLE_GENOME
constants storing the minimum and recommended sequence sizes for training.Genes
objects require a sequence_id
argument instead of using the internal sequence number.Mask
record coordinates in start-inclusive end-exclusive mode to follow Python conventions.importlib.resources
for managing test data.from_bytes
and from_string
constructors of Sequence
objects.Nodes._extract
(#21).TrainingInfo
objects corresponding to pre-trained models.calc_most_gc_frame
being inconsistent with the Prodigal implementation.score_connection_forward_start
not following the (weird?) behaviour from Prodigal (#21).Sequence._shine_dalgarno_mm
and Sequence._shine_dalgarno_exact
.Published by github-actions[bot] almost 2 years ago
Mask
record coordinates in start-inclusive end-exclusive mode to follow Python conventions.from_bytes
and from_string
constructors of Sequence
objects.Published by github-actions[bot] about 2 years ago
Sequence.gc_frame_plot
method to compute the max GC frame profile from Python.importlib.resources
for managing test data.Nodes._extract
.Published by github-actions[bot] about 2 years ago
metagenomic_bin
property to TrainingInfo
to support recovering the object corresponding to a pre-trained model.meta
attribute to Genes
to store whether genes were predicted in single or in meta mode.TrainingInfo
objects corresponding to pre-trained models.calc_most_gc_frame
being inconsistent with the Prodigal implementation.score_connection_forward_start
not following the (weird?) behaviour from Prodigal.Published by github-actions[bot] about 2 years ago
Sequence._shine_dalgarno_mm
and Sequence._shine_dalgarno_exact
.Genes
objects require a sequence_id
argument instead of using the internal sequence number.Published by github-actions[bot] about 2 years ago
vbicq
Arm intrinsic in the NEON implementation to combine vandq
and vmvnq
.Node
and Gene
objects from Python code.setup.py
not being applied to the linker.Published by althonos over 2 years ago
cpu_features
source files not being included in source distribution.Published by github-actions[bot] over 2 years ago
OrfFinder.train
can now be given more than one sequence argument to train on contigs from an unclosed genome.cpu_features
to v0.7.0
and added hardware detection of NEON features on Linux Aarch64 platforms.Published by github-actions[bot] over 2 years ago
pyrodigal.cli
now concatenates training sequences the same way as Prodigal does.Published by github-actions[bot] over 2 years ago
Stable version, to be published in the Journal of Open-Source Software.
pickle
protocol implementation for Nodes
, TrainingInfo
, OrfFinder
, Sequence
, Masks
and Genes
objects.Sequence
, allowing access to raw digits.__eq__
and __repr__
magic methods to Mask
objects.TRANSLATION_TABLES
and METAGENOMIC_BINS
are now exposed as constants in the top pyrodigal
module.list
buffers.Published by github-actions[bot] over 2 years ago
Gene.score
property to get the gene score as reported in the score data string.OrfFinder.find_genes
not producing consistent results across runs in meta mode (#13).OrfFinder.find_genes
returning Nodes
with incomplete score information.Published by github-actions[bot] over 2 years ago
mer_ndx
and score_connection
using dedicated implementations with better branch prediction.const
in C code where possible.embedsignature
directive._sequence.h
functions not being inlined as expected.Published by github-actions[bot] over 2 years ago
Sequence
code using inlined functions to increase performance when the strand is known.Nodes.copy
potentially failing on empty collections after trying to allocate 0 bytes.TestGenes.test_write_scores
failing on some machines because of float rounding issues.Gene.translate
ignoring the unknown_residue
argument value and always using "X"
.Pyrodigal.train
cause by memory not being freed after building the GC frame plot.Published by github-actions[bot] over 2 years ago
pyrodigal.OrfFinder
.Genes.write_scores
method to write the node scores to a file.Gene.__repr__
and Node.__repr__
methods to display some useful attributes.Sequence.__str__
method to get back a nucleotide string from a Sequence
object.Gene
data.Nodes._calc_orf_gc
reading nucleotides after the sequence end when computing GC content for edge nodes.pyrodigal.Pyrodigal
class (use pyrodigal.OrfFinder
instead).pyrodigal.Predictions
class (functionality merged into pyrodigal.Genes
).Published by althonos almost 3 years ago
load
and dump
methods to TrainingInfo
for storing and loading a raw training info structure.OrfFinder
pre-configured with a training info.-t
and -n
flags to the CLI.