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GenSpectrum / cov-spectrum-website

A web platform to detect and analyze variants of SARS-CoV-2
https://cov-spectrum.org
GNU General Public License v3.0
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ENH: apply Nextclade algorithm to the whole query without repeating nextcladePangoLineage #633

Open AnonymousUserUse opened 2 years ago

AnonymousUserUse commented 2 years ago

For example, if we want to view all Delta + Omicron recombinants, the standard query with pangoLEARN is: XD* | XF* | XS* | XAW* | XAY* | XBA* | XBC*; the query using Nextclade to identify lineages is: nextcladePangoLineage:XD* | nextcladePangoLineage:XF* | nextcladePangoLineage:XS* | nextcladePangoLineage:XAW* | nextcladePangoLineage:XAY* | nextcladePangoLineage:XBA* | nextcladePangoLineage:XBC*.

It would be good if the query using Nextclade can be shortened, e.g. by enabling users to apply Nextclade algorithm to the whole query without repeating nextcladePangoLineage. Some possible queries for that can be: nextcladePangoLineage:(XD* | XF* | XS* | XAW* | XAY* | XBA* | XBC*) or Nextclade: XD* | XF* | XS* | XAW* | XAY* | XBA* | XBC* or XD* | XF* | XS* | XAW* | XAY* | XBA* | XBC* alg:Nextclade

corneliusroemer commented 2 years ago

Very nice idea to overwrite the default like an environment variable @AnonymousUserUse!

I agree that it'd be great if it wasn't necessary to add nextcladePangoLineage every time.