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Llama code now runs on Codon. (with a 74 X improvement compared to Python).
https://github.com/dmahurin/llama2.codon/
https://github.com/tairov/llama2.py/pull/5
But, to get this to work chang…
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Right now codon mapping (to amino actids) are hardcoded [here](https://github.com/inc0/codone/blob/main/codone.py#L6). There may be variations between organisms. We should find a way to pull correct m…
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Dear mapnh developers,
I have been trying to reproduce the example provided in this tutorial (https://github.com/BioPP/supp-mat/tree/master/mapdNdS), but I am getting this error message I can not …
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Some genetic codes such as the Vertebrate Mitochondrial Code allow potentially different start codons / start amino acids. Is it possible to take this into account in diamond, e.g. by specifying that …
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Codon (https://github.com/exaloop/codon) aims to be "a high-performance and zero-overhead" Python compiler. Currently, we use PyInstaller (https://pyinstaller.org/) to create Windows builds, which ad…
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I tested the tool on a couple of protein sequences and for one of them the predicted DNA sequence is too complex for synthesis for both IDT and twist.
Twist has the following rules to determine wheth…
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https://github.com/exaloop/codon
I've remembered about this project, that claims to compile Python to machine code using LLVM.
But I'm not 100% sure it fits into the rules, will Python be accepted…
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In the following code, `foo` has an `Optional[A]` argument and does a check on it to see if is `None` or defined:
```py
class A:
pass
def foo(maybe_a: Optional[A]):
if maybe_a:
…
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The random_codon_table dictionary
https://github.com/modernatx/seqlike/blob/dde761ced5e3dcf86010d1e50abc3b268f794d8f/seqlike/codon_tables.py#L99
is biased for Isoleucine (I) with unequal probab…
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Please could the the docs include information on how to interpret the output of site_annotations()? I can't work out what the different levels of codon_nonsyn mean (effect?). I also can't quite work o…