pyrodigal
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althonos
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
Hi there @althonos , Thanks so much for your work on this tool, it's just great! I'm using `pyrodigal` to generate GBK files from some MAGs I curated that I...
Hello, I saw that pyrodigal can use different translation tables (issue #34), which is great! Do you know if pyrodigal can correctly identify selenocysteine insertions? (And pyrrolysine too) I have...
hello, something strange happens. when I use prokka, which uses prodigal to predict CDS,(prokka version 1.14.6) to annotate, the result showed that the position from 49243 to 50055 is entire...
I'm trying to replace `prodigal` with `pyrodigal` in my [VEBA binning-prokaryotic.py](github.com/jolespin/veba) module. I use stdin because I do some filtering on contig lengths w/ `seqkit` before I do gene calls...
Hello, Firstly, thanks for your work with Pyrodigal! I wasn't able to determine if Pyrodigal should be deterministic, if it is then ignore this ticket. I have an extremely rare...
While adding some tests to check for the GFF output (in order to fix #18) I noticed that the start score of some genes were deviating from the Prodigal reference...
Hi, as Prodigal v2.6.3, we observe with pyrodigal a difference in translation result for some start codon (TTG). >nuc sequence (Lactobacillus) TTGGGCATACCGGCTGAATACGTCTTATTCGACAGCTGTTTCTCTTCACCTAAAATGTTCTGGCAGCTGAAACAATTAGGGTTAGACAGCGTAGGCATGCTTAAGCGGACCAAGAAAGCTTATTATCGTTACCGTGGCCGACTTTATGATGTCAAAGGCCTGTACGAGCGCTTAGCTGCTTCCAAAATGCGTCAAAAAGAAGACTATCCCTATAGCAGCGTGGTCGAACCTGAATATCAGGGACATGTTTTCCAAATTAGATTAGTCTATGTCACTAAGCGCGGCGGTAAAGGAAAATATTTGGTACTGGTAACCACGCAATACAAGCTGCGATCAAAGTATTGCACGTCTTCTATGACAAGTGGAACAGAGCTTATAATCATGTCATAA >Prodigal / pyrodigal output MGIPAEYVLFDSCFSSPKMFWQLKQLGLDSVGMLKRTKKAYYRYRGRLYDVKGLYERLAASKMRQKEDYPYSSVVEPEYQGHVFQIRLVYVTKRGGKGKYLVLVTTQYKLRSKYCTSSMTSGTELIIMS* >Expected sequence (Expasy...
Some links to the GeneFinder documentation page were still pointing to the old OrfFinder docs. I also noticed that the [Thread-safety](https://github.com/althonos/pyrodigal?tab=readme-ov-file#-thread-safety) code snippet initializes a `gene_finder` variable but later calls...
The `--no-stop-codon` behaviour is confusing right now, as it is set to `True` by default but the stop codons are being written. This PR fixes that by changing the default...
Hi @althonos , I hope you've been well mate! I have an issue/discussion to raise based on some related discussions here on my circular contig reorientation tool Dnaapler https://github.com/gbouras13/dnaapler/issues/90 ....
