-
Notifications
You must be signed in to change notification settings - Fork 94
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Making seqrepo optional #624
Comments
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. |
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. |
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]
, notpip install hgvs
.The text was updated successfully, but these errors were encountered: