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quinlan-lab / pathoscore

pathoscore evaluates variant pathogenicity tools and scores.
MIT License
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add clinical utility table for a list of provided genes #38

Closed jimhavrilla closed 6 years ago

jimhavrilla commented 6 years ago

accuracy * number of variants scored for each gene

jimhavrilla commented 6 years ago

make table scrollable, sorted by score (optionally) on the command line we want it to work something like: python pathoscore.py evaluate --functional --prefix clinvar -s CCR -s CADD -s GERP -s MPC -s REVEL --suffix --goi list_of_genes.txt pdf pathogenic.vcf.gz benign.vcf.gz where goi is "genes of interest" and expects a file with a single-column list of genes for which to score clinical utility

arq5x commented 6 years ago

Nice work. The ability to sort the table by each tool's scores (asc, desc) and to scroll/paginate for long lists would be great. Lastly, I think you just need 3 digits of precision after the decimal once you dig into the potential issues with the way the score is calculated.

jimhavrilla commented 6 years ago

Doesn't seem like sorting by tool is a feature plot.ly is capable of adding. I would probably have to use some other software to accomplish that. Scrolling is inherent in plot.ly though.

arq5x commented 6 years ago

I assume you can bring in external JS libraries? Perhaps: http://tristen.ca/tablesort/demo/

jimhavrilla commented 6 years ago

completed by #39