ClinVar Search helps extracts data from the ClinVar page using EUtils package.
To get all the short variants i.e. Variants < 50kb (SNV and Short INDELS).
Also pass a comma seperated list of words you want to search to scrape the ClinVar ID page for those words.
The outPrefix parameter takes the name of the output and it will be generate results in the same folder where the script is.
Make sure to pass a csv file with column name 'coordinates' and the genomic coordinates in GRCh38:chromosome:start:end format.
Packages Required:
- pandas
- ratelimit
python clinvarSearch.py --inputFile <csv-file> --word <any-word-to-search> --outPrefix <prefix-for-output>This code uses concurrent.futures for simulateneously get the ClinVar ID for multiple Genomic Coordinates at once, and since EUtils has api call limit that is 3 query per second so ratelimit package is used to control that flow.