DnaChisel

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Question: No boost for AllowPrimer

1

I noticed some objectives such as "dnachisel.builtin_specifications.AllowPrimer" do not have any boost parameter. How are they balanced with other objectives people might specify concurrently? Many objective options have the boost...

jlerman44

This PR updates the __init__.py to expose AvoidHeterodimerization.

maxall41

Question: Avoid sequence of codons

9

I have several sequences of codons that I want to remove, not necessarily a pattern within the whole sequence. The codon sequences are all 3 long (9 NT). I am...

kmcgrathgenerate

CodonOptimize replaces a codon with non-synonymous codon

2

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 =...

dadddda

GCContent module is compatible with numpy 2.1.0.

1

Hello, This PR fixes #83 . The compatibility issue comes from the fact that the `gc_content` function when not given a window size returns a scalar. To ensure full backwards...

ondrej-sladky-eligo

NumPy 2.0 and up are not compatible with the use of nonzero function in some evaluate methods

2

Should limit numpy requirement to breaches_starts = wstart + (breaches > 0).nonzero()[0] E ValueError: Calling nonzero on 0d arrays is not allowed. Use np.atleast_1d(scalar).nonzero() instead. If the context of this...

bwvogler

Sometimes you have an unsolveable optimization problem running in a subprocess. It's useful to allow NoSolutionError to be pickleable so that the exception can propagate back to the main process....

tdsmith

Question: how to get under-optimal sequences during optimization?

2

Thank you for your work! I want to get sequences which are under-optimal, and I've noticed that in issue #27 and #39 that DNAChisel is not developed to generate multiple...

wyattxuanyang

Hi Peter, I finally learned how to use DNAchisel and found it very useful, all here: https://github.com/ewallace/Emergomyces_constructs_2025 For my applications needing codon usage tables for specific subsets of genes in...

ewallace

Consequences of partial CDS optimization

1

Hi there, If this isn't the right place to ask, please let me know! In our lab, we're utilizing a library of modules for the N and C terminals because...

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