Make the HGVS parser as a separate package
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I was wondering if it's possible to release the HGVS parser as a separate package.
My use case is to read and parse a given variant's existing HGVSc and HGVSp annotation (from VEP etc). hgvs.parser.Parser nailed this problem by implementing a solid grammar, which is much better than hacking a regex-based solution. So my use case only requires the parser and doesn't really need to normalize or 'liftover' the HGVS strings. If my understanding is correct, hgvs only requires parsley and some biocommons' data structures to get the parser working. This will shrink down the total dependencies by quite a bit (such as SQL and database related packages). The advantage of keeping a smaller dependencies is that the downstream user requires less setup.
So I was wondering if it's possible to release hgvs modules individually. I don't know if the developers here are interested to make hgvs a bioconda package. If so, I am happy to help :)
Thanks for making this wonderful tool!
There's good separation of the parser and models from the algorithmic components, so splitting the package is possible and useful. However, it'd be a bit of work that I don't have time for.
I'll leave this open to track interest and perhaps future work. PRs welcomed!
Sounds good! I will give it a try and if it works I will update here. Thanks again.
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