Making seqrepo optional

[kislyuk]

biocommons.seqrepo pulls in a lot of dependencies. Since it is optional, can this be reflected in the setuptools configuration by using an extras flag? https://setuptools.pypa.io/en/latest/userguide/dependency_management.html#optional-dependencies

This way seqrepo would only be pulled in when running pip install hgvs[seqrepo], not pip install hgvs.

[reece]

Yes, that works for me. I'll queue up for 1.6. No ETA.

Can you elaborate on your use case that doesn't require seqrepo? Do you use hgvs only for parsing and formatting? The rationale for requiring it was that sequence validation is extremely common in hgvs.

[kislyuk]

Thanks.

Yes, for our internal variant pipelines, we use hgvs only for parsing and formatting. Additionally, we are receiving variants from multiple upstream clinical sequencing labs that each have their own pipelines and variant databases. Each variant has a gHGVS, cHGVS and pHGVS field, including SVs. I'm looking to define a lightweight process to load and validate the HGVS strings, linting them against nomenclature best practices described in https://varnomen.hgvs.org/, but I don't want to pull the reference sequence since that seems overkill and would either add a lot of size to the deployment package, or a lot of latency to the validation process. I was actually going to reach out to you to ask for any recommendations for implementing such a linting process.