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I would like to train Augustus on three eukaryotic genomes. I have the following for each:
- a repeat-masked FASTA
- a GFF file of coding regions, exons, start codons, and stop codons
When I feed…
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Dear developers,
It seems to me that Codon is unable to perform a simple conversion from a list to a tuple. Here is a minimal example:
```python
l = [1, 2]
t = tuple[int, int](l)
print(t)
``…
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Are the commands not supposed to be able to operate on as many things as possible? I think deleting and repairing codons (rgl values) is pretty obvious, but what about removing ugos, digesting waste, …
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The permissible Codons translations can be expanded by manually copying the wikipedia options and using the [codons-usage-tables](https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables) module…
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**Is your feature request related to a problem? Please describe.**
We currently do not properly handle SCR, e.g., in SELENON.
**Describe the solution you'd like**
Address this issue.
**Des…
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Hi,
I am trying to repeat part of your work to generate diverse coding sequence, but I could not find the host codon usage table, such as CLIB_release.csv for the Y. lipolytica or files for the E. co…
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Hi, love the project!
I recently started implementing a ray tracer as an exercise for trying out Codon. After a while, I was curious to try and make the code work with vanilla Python and PyPy, and …
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Dear Philipp,
It's a wonderful soft!
When we build a phylogenetic tree, we often remove 3rd codon. Could you mind adding some optional like this?
Best wishes,
Deyuan
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### Compiler name
Codon
### Compiler version
0.16.3
### Compiler language
Python
### Compiler homepage
https://github.com/exaloop/codon
### Motivation
I'd like to be able to see the differenc…
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This ticket will include scoping iterations for the VEP widget on the variant page.
Please note that at time of issue opening, the variant index data/API is not completed e.g. the data team is work…