Comments (3)
There are several ways to up speed computations, but that depends on your project (do you have a minimal example you could share?).
The verify_constraints
method is probably called on every subsequence so it is not surprising for it to be a bottleneck. The surest way to speed up computations is to use the coarse_grain
/fine_grain
parameters, or the A* parameter (both approaches reduce the number of subsequences evaluated, and correspond to slides 220-250 of this slideshow).
Another optimization consists in using memoize=True
in CommercialDnaOffer
and DnaAssemblyStation
to cache the computations of price (and assembly plans) for subsequences. but that will only speed things up if you are doing multi-level assemblies, or if you are evaluating several sequences (with common subsequences) on a same supply network.
I understand that the documentation is not as good as it could be so don't hesitate if you have more questions.
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Thank you @Zulko! I will try what you mentioned
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To be honest, code comments helping a lot, so you are a bit humble on saying that documentation is not sufficient :)
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Related Issues (12)
- dealing with circular DNA HOT 18
- Example of using PartsLibrary with Gibson assembly method HOT 2
- File Not Found Error during assembly_report execution HOT 2
- What to do when Gibson assembly Station is refused : Apologies to put a routine use question as an issue HOT 10
- Contact Zulko HOT 7
- SBOL => Automation MoClo Assembly tool => Optimal assembly report HOT 2
- Does the PartsLibrary work for circular sequences? HOT 3
- What role cut_spread_radius plays in circular sequence decomposition? HOT 1
- Q: Any specific reason why PcrExtractionStation not using the PartsLibrary? HOT 1
- Bug: Max length initialisation HOT 2
- Bug: When quote.assembly_plan is None
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