`Primer3` should accept a variant lookup `Path`

fulcrumgenomics / prymer

Python Primer Design Library

https://prymer.readthedocs.io/en/latest/

MIT License

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`Primer3` should accept a variant lookup `Path` #53

Open msto opened 1 week ago

msto commented 1 week ago

Much like Primer3 accepts a Path to the input FASTA, it would be more ergonomic if the class accepted a Path to a VCF instead of requiring the user to construct a VariantLookup.

emmcauley commented 1 week ago

We have two VariantLookup objects and corresponding constructors: one is recommended for smaller VCFs and one is recommended for bigger VCFs. I'm envisioning that we could take a path to a VCF, determine the appropriate constructor, and construct the VariantLookup object under the hood.

@msto: -do you agree with my thoughts above? Did I miss anything? -if so, what do you think is the best way for us to check the given VCF path to see which constructor would be the appropriate one to call?

emmcauley commented 1 week ago

plan:

add to the Primer3 constructor, a list of VCFs, and a boolean flag (should we load into memory or query every time we need something?) -- the bool will trigger what variant lookup to build; but the default will be the disk-based one

msto commented 1 week ago

Yes, that's exactly what I had in mind 🙂