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isabelrem / 2023-Software-Development-Assessment

MIT License
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Extract exon boundaries from VV API output and input into the .bed file output #41

Closed TomLivesey-UoM closed 9 months ago

TomLivesey-UoM commented 9 months ago

I've extracted the exon boundaries for each gene and written them into the bed file and bedfile json (in a branch called 41-exon-boundaries) - from VV I've got the exon boundaries in both genomic coords and coords within the mane_select transcript being used. At the moment I'm using the transcript coords for the boundaries but this can be changed easily if we want to use the genomic ones instead (probably a question to ask users).

TomLivesey-UoM commented 9 months ago

I am currently resolving the above choice by getting the user to input their choice of transcript or genomic coordinates. Their choice will be saved in the produced json and will affect the information given in the .bed file (if they choose genomic coordinates the transcript will not be given as the information has not come from it).