Make full SnapGene data integration

[merv1n34k]

Hey!

I really liked your project, but I would like it to have some key features added which would let me and my team integrate it in our daily workflow.

I think I am able to contribute for the parts I am plan to add, but it would be nice to share the work if you're interested. I will separate them into several issues.

Cut to the chase, this issue is about implementing a full SnapGene integration, by means of complete data integration from SnapGene files, which contain:

1. Sequences
2. Primers
3. Features
4. Alignments data (in ZTR format)
5. History tree and nodes (PCR, cloning, modifications, etc)

Other parts are internal SnapGene data and in (almost) all cases can be simply omitted without any problems.

Implementation proposition

I suggest to implement a module/util which will help us to:

1. Read SnapGene files, extract all the data we can
2. Transform it into OpenCloning LinkML data scheme
3. Let user access the history as a properly defined OpenCloning workflow (e.g. transform SnapGene history into OpenCloning data scheme)
4. Export OpenCloning schemes into full SnapGene files (with history, sequences, etc.)

I suggest using the library I am working on - sgffp, which as of now can read/decode all the data we need from SnapGene and (yet) a minimalistic writer to original SnapGene file format.

Roadmap

• feat: finalise sgffp lib, make a production ready reader/writer
• feat: implement a translation scheme for SG to OC and vice versa
• feat(backend): add a util/module for importing SnapGene data
• feat(frontend): update UI/UX for working with SnapGene files
• fix: add example SnapGene files
• docs: update documentation
• TBA

I am quite tight on schedule right now, but I think I could try to start working on it in Q1-Q2 of 2026. I am open to suggestions, feel free to reach me out - merv1n@proton.me.

[manulera]

Hi @merv1n34k thanks for your message. Yes, that would be really nice, and you can use the library provided to work directly with pydantic objects mapping to the opencloning-linkml model:

However, unless you can read parent sequences as mentioned here
IsaacLuo/SnapGeneFileReader#5 I am not sure it would be possible. Did you figure out how to extract the sequences of ancestors?

[merv1n34k]

@manulera But of course!
As I have mentioned it previously, to build a proper tree of modifications you need a history tree, each tag in the tree references a history node, which contains all information, including sequences.

I will take a closer look at tree implementation and will create a spec of SnapGene history structure. Seems it will be a good start aside from finalizing SnapGene read/write lib.

[manulera]

Right, looking forward to it