Little repo to explain how to combine my two ClinVar repos for extracting and plotting submission informations.

conda env export from my working environment

• download ClinVar release of your choice

wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_00-latest.xml.gz

• extract gzip, if your are low on space you can also run the code directly on the .gz

gunzip ClinVarFullRelease_00-latest.xml.gz

1 - notebook for CLinVar parsing)

• code reads in the ClinVar xml and extracts detailed infos about submissions
• runs ~ 90 minutes, depending on the number of cpu's
• outfile ~ 350mb in size

2 - notebook for plotting

• code reads in outfile from 1. --> dataframe can be filtered for the genes and variants of interest
• creates dict that define the single frames of the final video
• creates all the figure
• render video