search

BjornFJohansson / pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
Other
166 stars 45 forks source link

Manually continue pcr method #117

Closed ngamarra closed 1 year ago

ngamarra commented 1 year ago

Hello!

I am having a minor issue when attempting pcr. When I attempt to run in python 3.7 in a jupyter notebook it raises pdb at the following lines.

> /Users/ngamarra/Library/Python/3.7/lib/python/site-packages/pydna/amplify.py(528)pcr()
-> if hasattr(s, "watson"):
(Pdb) c
> /Users/ngamarra/Library/Python/3.7/lib/python/site-packages/pydna/amplify.py(527)pcr()
-> breakpoint()
(Pdb) c
> /Users/ngamarra/Library/Python/3.7/lib/python/site-packages/pydna/amplify.py(528)pcr()
-> if hasattr(s, "watson"):
(Pdb) c
...

This isn't too annoying for one amplicon, but I am trying to amplify several hundred sites in batch and having to manually continue is a bit of pain...

BjornFJohansson commented 1 year ago

Hi, can you tell me what version of pydna and biopython you are using? There might have been a version where I left some breakpoints in the code.

BjornFJohansson commented 1 year ago

@ngamarra updating pydna should solve this issue.

ngamarra commented 1 year ago

Done! Works great! Thanks!!