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Optimizing a gene coding sequence with a custom codon table using the DnaChisel version **3.2.11** gives unexpected output.
This is the snippet from the Python code used:
```python
problem = DnaO…
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Collecting codon
Using cached codon-0.0.1.tar.gz (21 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully…
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On a Gentoo box with LLVM 18.1.8 the build aborts with:
```
[ 77%] Building CXX object CMakeFiles/codonc.dir/codon/parser/visitors/typecheck/assign.cpp.o
[ 77%] Building CXX object CMakeFiles/cod…
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was hoping someone could help out with the following error:
```
codon.codon_jit.JITError: /home/ubuntu/.pyenv/versions/3.11.1/envs//lib/python3.11/site-packages//file.py:19:2: no module named 'codo…
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I work on Gram-positive actinobacteria, which can frequently encoded alternative starts. I've noticed some genes are annotated with a wrong start (frequently too long to comply with an ATG start inste…
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At least in production, we currently include stop codons (`*`) at the end of our protein sequences. I think to me this feels quite unexpected. NCBI doesn't seem to do it: https://www.ncbi.nlm.nih.gov/…
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```sh
(base) canftin@DESKTOP-4QK14RE ~/workspace/codon_ws/codon/build> gdb -args codon run ../.vscode/debug/test_fib.py
GNU gdb (Ubuntu 15.0.50.20240403-0ubuntu1) 15.0.50.20240403-git
Copyright …
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Hello!
I'm having a slight issue with the annotations generated by EGAPx. When I translate the CDS into a protein sequence, I'm seeing a lot of premature stop codons. This is a species where I am s…
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Creating test file
```python
# test.py
import os
os.environ.setdefault("lala", "tralala")
```
Running with `codon`
```sh
$ codon run test.py
test.py:3:1-41: error: 'EnvMap' object has no …
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I'm hoping to understand how to interpret a result in which HyPhy MEME detects positive selection at a codon, but with 0 branches under selection. An example is present in the following analysis outpu…