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PatrickWeller / PanelPal

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Issue20 Change Bed file generation to use Variant Validator Exon coordinates #33

Closed madysonic closed 2 weeks ago

madysonic commented 2 weeks ago

Issue20 Change Bed file generation to use Variant Validator Exon coordinates. Relates to user story #8.

Two functions to extract transcript/exon information from the Variant Validator API, and a third function to generate a bed file based on a list of genes.

Bed file function requires a list of genes and a panel name as input. This will need to come from the Panel App API functions.

madysonic commented 2 weeks ago

To test, can use the following:

gene_list = ["PRKAR1A", "PDE4D", "GNAS"] panel_name = "R293" genome_build = "GRCh38"

generate_bed_file(gene_list, panel_name, genome_build)

Next step will likely be integrating with Panel App API functions to generate these three input variables.

PatrickWeller commented 2 weeks ago

Nice clear comments, doc strings and variable names. Testing works. Happy to merge