Releases: althonos/pyrodigal
Releases · althonos/pyrodigal
v1.1.1
v1.1.0
Changed
OrfFinder.train
can now be given more than one sequence argument to train on contigs from an unclosed genome.- Updated
cpu_features
tov0.7.0
and added hardware detection of NEON features on Linux Aarch64 platforms.
v1.0.2
v1.0.1
Changed
pyrodigal.cli
now concatenates training sequences the same way as Prodigal does.
v1.0.0
Stable version, to be published in the Journal of Open-Source Software.
Added
pickle
protocol implementation forNodes
,TrainingInfo
,OrfFinder
,Sequence
,Masks
andGenes
objects.- Buffer protocol implementation for
Sequence
, allowing access to raw digits. __eq__
and__repr__
magic methods toMask
objects.
Changed
- Optimized code used for region masking to avoid searching for the same mask repeatedly.
TRANSLATION_TABLES
andMETAGENOMIC_BINS
are now exposed as constants in the toppyrodigal
module.- Refactored connection scoring into different functions based on the type (start/stop) and strand (direct/reverse) of the node being scored.
- Changed the growth factor for dynamic arrays to be the same as the one used in CPython
list
buffers.
v0.7.3
v0.7.2
Changed
- Improve performance of
mer_ndx
andscore_connection
using dedicated implementations with better branch prediction. - Mark arguments as
const
in C code where possible.
Fixed
- Signatures of Cython classes not displaying properly because of the
embedsignature
directive. _sequence.h
functions not being inlined as expected.
v0.7.1
Changed
- Rewrite internal
Sequence
code using inlined functions to increase performance when the strand is known.
Fixed
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 theunknown_residue
argument value and always using"X"
.- Memory leak in
Pyrodigal.train
cause by memory not being freed after building the GC frame plot.
v0.7.0
Added
- Support for setting a custom minimum gene length in
pyrodigal.OrfFinder
. Genes.write_scores
method to write the node scores to a file.Gene.__repr__
andNode.__repr__
methods to display some useful attributes.Sequence.__str__
method to get back a nucleotide string from aSequence
object.
Changed
- Use a more compact data structure to store
Gene
data.
Fixed
Nodes._calc_orf_gc
reading nucleotides after the sequence end when computing GC content for edge nodes.
Removed
pyrodigal.Pyrodigal
class (usepyrodigal.OrfFinder
instead).pyrodigal.Predictions
class (functionality merged intopyrodigal.Genes
).