jjti
commented
1 year ago I really like the idea of adding primer visualizing to SeqViz. There's an open feature request for that: https://github.com/Lattice-Automation/seqviz/issues/232. It's also a standard feature in a lot of visualizers.
SeqViz used to have it awhile ago, but I removed it from circular/linear viewers because it was pretty bugged and the code was difficult to maintain.
Regarding this PR in particular though, I'm not sure we want to add design into SeqViz. Or modals. As much as possible my hope is that SeqViz remains strictly visualization/presentation focused. That's for a couple reasons but mainly:
- to avoid adding any opinionated business logic about how plasmids/primers/annotations are created/annotated. I think there's a lot of "best practices" and we'd increase the size of the parameters by quite a bit if we tried to support all of them
- to keep the LOC in SeqViz as small as possible
- to keep the number of dependencies in SeqViz as small as possible, eg to enable a migration to something other than React if that were to ever happen: https://github.com/Lattice-Automation/seqviz/issues/178
What we could add though is something like:
interface Primer extends NameRange {
}
interface SeqVizProps {
primers?: []Primer;
}
digithed
I was exploring SeqViz and thought that a feature where a user could design primers easily based on a selected sequence region might be useful. This is just a proof of concept, but it provides an easy way to provide primers for a region based on the ideal melting temp, length, gc content, etc. There are a lot of primer design tools but having this would have it already integrated into the viewer.
This is WIP because it's a basic implementation and it is more of an exploratory feature, users can only design one primer set/target at a time, so if this is something we might want I can work on it further.