Update vcf2gvf.py to work with new gene positions JSON format

cidgoh / nf-ncov-voc

A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.

MIT License

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Update vcf2gvf.py to work with new gene positions JSON format #143

Closed miseminger closed 10 months ago

miseminger commented 10 months ago

older commits (first 2) in this pull request for creating the old mpox JSON with colors can be ignored
in the future, will need another way to select which of overlapping CDS regions to use for annotation for SARS-CoV-2 (for now, choosing the one with a "protein_alias" key is a temporary fix)