Scrape VOCs, etc from more agencies

[atc3]

• WHO: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/
• ECDC: https://www.ecdc.europa.eu/en/covid-19/variants-concern
• PHE: https://www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers

For PHE, find the latest HTML report, go to that link, then scrape the table on the resulting page

[atc3]

Updated task:

• Write separate webscrapers for each agency, output into individual JSON files. Not crucial that we scrape every single metadata column - only requirement is that we get the pair of PANGO lineage + classification (i.e., B.1.1.7 + VOC)
• Write a snakemake rule to combine results from each individual webscraper. Aim for a compact CSV format, where rows = PANGO lineages and columns = agencies, and cells = classification (VOC, VOI, etc).
• This CSV can be exported into web-friendly JSON with .to_json(orient='records'). This will produce an array of {"lineage": "B.1.1.7", "WHO": "VOC", "CDC": "VOC", ...}
• Separate snakemake rule for pulling PANGO lineage – WHO convention map. i.e., "B.1.617.2": "Delta"

[atc3]

Additional cleaning:

• If multiple lineages are defined in one option, split them into two
• Remove additional mutations in the definition. i.e., B.1.1.7 + P384L
• Collapse duplicate lineages by keeping the most severe one. i.e., if one lineage is both VOC and VOI, then drop the VOI entry but keep the VOC one.

[atc3]

Closed by #357