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 althonos almost 3 years ago
pyrodigal
command line script exposing a CLI mimicking the original prodigal
binary.write_gff
, write_genes
and write_translations
methods to pyrodigal.Predictions
to write the predictions results to a file in different formats.pyrodigal.Pyrodigal
class to pyrodigal.OrfFinder
.setup.py
build different SIMD implementations with the same set of feature flags, causing compilers to re-optimize the SIMD implementations.Published by althonos about 3 years ago
setup.py
not detecting SSE2 and AVX2 build support because of a linker error.Illegal Instruction: 4
bug on older CPUs.Published by althonos about 3 years ago
cpu_features
.Published by althonos about 3 years ago
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).Prediction.gc_cont
number directly from the start node instead of the text representation to get full accuracy.Published by althonos about 3 years ago
Prediction.translate
not translating the last unknown codon properly for genes on the direct strand.Published by althonos about 3 years ago
Pyrodigal.train
return a reference to the newly created TrainingInfo
for inspection if needed.add_nodes
and add_genes
to use a growable array instead of counting and pre-allocating the C arrays.Published by althonos about 3 years ago
Gene
properties to access the scorePyUnicode
macros when reading or creating a string containing a nucleotide or a protein sequence.str
given as input to Pyrodigal.find_genes
.Gene.translate
.Pyrodigal.find_genes
and Gene.translate
not behaving like Prodigal when handling sequences with unknown nucleotides.Published by althonos over 3 years ago
pyrodigal.TrainingInfo
class exposing variables obtained during training as an attribute to Pyrodigal
, Gene
and Genes
instance.Pyrodigal.find_genes
and Pyrodigal.train
instead of requiring str
sequences.Gene.translate
with a non-default translation table was being translated at the same time as a Pyrodigal.find_genes
call.Published by althonos over 3 years ago
pyrodigal.tests
module and can be run after a site install.Pyrodigal.find_genes
stalling on sequences shorter than 3 nucleotides.Published by althonos over 3 years ago
Published by althonos over 3 years ago
Published by althonos over 3 years ago
meta
mode on a sequence too small to have any dynamic programming nodes.Published by althonos over 3 years ago
Published by althonos almost 4 years ago
libprodigal
against the _pyrodigal
extensionPublished by althonos almost 4 years ago
Published by althonos almost 4 years ago
README.md
.Typing :: Typed
classifier to the PyPI metadata.Published by althonos about 4 years ago
Pyrodigal
methods