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BjornFJohansson / pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
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Error in annotation for PCRs #279

Closed manulera closed 2 weeks ago

manulera commented 1 month ago

Hello @BjornFJohansson I noticed an error when transferring features from the PCR template to the product. I have fixed it in this commit.

See amplify and utils.

Basically, if the primer had a tail, the features were not being shifted. Will add a test for this

BjornFJohansson commented 1 month ago

Is this a part of a coming merge?

I made a branch called primerdesignbug, not sure how to link it here. It has a solution to allow the original example to run with very short primers. I saw that the example was updated with longer primers which is maybe a good idea. I would still want the original example to run.

manulera commented 1 month ago

Hi @BjornFJohansson,

The fix is in an upcoming branch yes. As of now it's in the linked commit part of the PR #278

I made a branch called primerdesignbug, not sure how to link it here. It has a solution to allow the original example to run with very short primers. I saw that the example was updated with longer primers which is maybe a good idea. I would still want the original example to run.

From what I can see in primerdesignbug, the fix you included is different from what I was mentioning here, so I thin you can probably just create a PR for that.

manulera commented 2 weeks ago

This was still failing in circular sequences. I fixed that with this new PR