Comments (2)
The fix package seems to be updating the weights with more data, we should consider putting all the functions which updates those amino acid weights in the same struct for a less leaky abstraction
Could you be more specific on the line? I don't recall it updating the weight table with more data, just getting out which new codon it should use based on the data, then applies biases.
Agreed it should be updated though.
from poly.
I assumed it was updating the weights with some other heuristics but after reading more carefully I see it's not, I thought it would be a duplicate of the codon picking mechanism in optimize
If I understand well the package is using the weighted AAs to get the highest weighted codon in a set of potential codon replacements gotten with other methods (gc bias ect...) here.
I don't really see a straightforward way to get rid of this in a way that make things noticably better since it's using the fix.Change
struct so I think it's best to leave things as is 👍
from poly.
Related Issues (20)
- Reduce number of reviewers necessary for merge HOT 5
- Document all these workflow changes in `CONTRIBUTING.md` HOT 1
- Concurrent mashing HOT 2
- Genbank parser doesn't handle feature attributes with colliding names. HOT 5
- Genbank location parser breaks on parsing this location. HOT 1
- Genbank import and export from JSON should include feature sequences HOT 2
- Simulate enzyme methylation through lowercasing
- Poly n Plannotate HOT 5
- Compressed Seqhash
- Tutorial and example tests for refactored golden gate cloning HOT 1
- Proposal: create a distance package for Mash, Geometric string distance, and other distance metrics. HOT 4
- Add example test to MASH HOT 1
- Remove start codon check HOT 1
- Each fragment in a PCR amplification should have a circular tag HOT 1
- Proposal: Create a biological reviewers group HOT 2
- Create nightly, dev, and stable build channels HOT 1
- Proposal - New external package - rebased HOT 2
- Genbank parser needs heavy refactor or a rewrite HOT 8
- Turn on `revive` linter in golangci config HOT 1
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from poly.