When the backbone contains 2 sets of correctly oriented enzyme sites (BsaI and BsmBI), then autoselect may not correctly choose the one we want to use.
This can be addressed by specifying an enzyme for each assembly:
assembly_plan = dc.AssemblyPlan.from_spreadsheet(
name="Assembly",
path=assembly_plan_path,
assembly_class=dc.Type2sRestrictionAssembly
)
for assembly in assembly_plan.assemblies:
assembly.enzyme = "BsaI"
so this is not an issue in DNA Cauldron, but causes a bug in CUBA where the enzyme selected in the dropdown menu is ignored.
A possible solution is to make a note about this in the documentation and add the above code in CUBA.
When the backbone contains 2 sets of correctly oriented enzyme sites (BsaI and BsmBI), then autoselect may not correctly choose the one we want to use. This can be addressed by specifying an enzyme for each assembly:
so this is not an issue in DNA Cauldron, but causes a bug in CUBA where the enzyme selected in the dropdown menu is ignored.
A possible solution is to make a note about this in the documentation and add the above code in CUBA.