Releases: althonos/pyrodigal
Releases · althonos/pyrodigal
0.6.3
Added
pyrodigal
command line script exposing a CLI mimicking the originalprodigal
binary.write_gff
,write_genes
andwrite_translations
methods topyrodigal.Predictions
to write the predictions results to a file in different formats.- Implementation for masking regions of unknown nucleotides in input sequences.
Changed
- Renamed
pyrodigal.Pyrodigal
class topyrodigal.OrfFinder
.
Fixed
setup.py
build different SIMD implementations with the same set of feature flags, causing compilers to re-optimize the SIMD implementations.
0.6.2
Added
- Sphinx documentation with small install guide and API reference.
Fixed
setup.py
not detecting SSE2 and AVX2 build support because of a linker error.
Changed
- Build OSX extension without AVX2 support since runtime detection of AVX2 to avoid the
Illegal Instruction: 4
bug on older CPUs.
0.6.1
0.6.0
0.5.4
Added
Prediction.confidence
method to compute the confidence for a prediction like reported in Prodigal's GFF output.Prediction.sequence
method get the nucleotide sequence of a predicted gene (#4).
Changed
- Replaced internal storage of input sequences to use a byte array instead of a bitmap.
Fixed
- Extract
Prediction.gc_cont
number directly from the start node instead of the text representation to get full accuracy. - Prodigal bug causing nodes on the reverse strand to always receive a penalty instead of penalizing only small ORFs (hyattpd/Prodigal#88).
0.5.3
0.5.2
Changed
- Make
Pyrodigal.train
return a reference to the newly createdTrainingInfo
for inspection if needed. - Reimplement
add_nodes
andadd_genes
to use a growable array instead of counting and pre-allocating the C arrays.
Fixed
- Inconsistent handling of unknown nucleotides in input sequences and gene translations.
0.5.1
Added
- Additional
Gene
properties to access the score
Changed
- Use more efficient
PyUnicode
macros when reading or creating a string containing a nucleotide or a protein sequence. - Release the GIL when creating a bitmap for an
str
given as input toPyrodigal.find_genes
. - Release the GIL when creating the protein sequence returned by
Gene.translate
.
Fixed
Pyrodigal.find_genes
andGene.translate
not behaving like Prodigal when handling sequences with unknown nucleotides.
0.5.0
Added
pyrodigal.TrainingInfo
class exposing variables obtained during training as an attribute toPyrodigal
,Gene
andGenes
instance.- Support for passing objects implementing the buffer protocol to
Pyrodigal.find_genes
andPyrodigal.train
instead of requiringstr
sequences.
Fixed
- Potential data race on training info in case a
Gene.translate
with a non-default translation table was being translated at the same time as aPyrodigal.find_genes
call. - Spurious handling of Unicode strings causing potential issues on platform using a different base encoding.