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cov-lineages / constellations

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Comments in site definitions are problemaic #45

Closed nekrut closed 2 years ago

nekrut commented 2 years ago

Lines like this (BY.2-like definition):

        "nuc:T22200G # spike:V231G # but this seems to be wrong aa ref allele",

brake all automated parsing of these json files. Perhaps a dedicated comment tag is needed. This has very bad implications for anyone who automates definition retreaval.

rmcolq commented 2 years ago

I deliberately added comments in such a way that the file could be parsed by the python json module. What automatic parsing are you doing?

I have reverted this change pending a major release

nekrut commented 2 years ago

I convert coordinates into genomic coordinates and then validate every amino acid or nucleotide change.

rambaut commented 2 years ago

We will be implementing this at some point soon. But we will give warning that downstream pipelines will need to be able to respect comments prefixed by #.