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AttributeError: 'NoneType' object has no attribute 'startswith' #231

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ktmeaton opened this issue Feb 21, 2023 · 0 comments
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AttributeError: 'NoneType' object has no attribute 'startswith' #231

ktmeaton opened this issue Feb 21, 2023 · 0 comments
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ktmeaton commented Feb 21, 2023

In rule sc2rf_recombinants.

  File "ncov-recombinant/sc2rf/postprocess.py", line 998, in main
    while max_lineage.startswith("X") or max_lineage == "Unassigned":

Querying cov-spectrum for region 22200:24469
Starting new HTTPS connection (1): lapis.cov-spectrum.org:443
https://lapis.cov-spectrum.org/open/v1/sample/aggregated?fields=pangoLineage&nucMutations=T22200G,G22578A,C22674T,T22679C,C22686T,A22688G,G22775A,A22786C,G22813T,T22882G,T22917G,G22992A,C22995A,A23013C,T23018C,T23019C,A23055G,A23063T,T23075C,A23403G,C23525T,T23599G,C23604A,C23854A,G23948T,A24424T,T24469A

I think it's the null that's the problem

{"errors":[],"info":{"apiVersion":1,"dataVersion":1676913536,"deprecationDate":null,"deprecationInfo":null,"acknowledgement":null},"data":[{"pangoLineage":"XAY.3","count":1},{"pangoLineage":"XAY.1","count":9},{"pangoLineage":"XAY.2","count":18},{"pangoLineage":"Unassigned","count":5},{"pangoLineage":"XBB.1.5","count":1},{"pangoLineage":"XAY.1.2","count":5},{"pangoLineage":"BA.2.10.1","count":2},{"pangoLineage":"XAY.1.1","count":14},{"pangoLineage":null,"count":5}]}
@ktmeaton ktmeaton self-assigned this Feb 22, 2023
@ktmeaton ktmeaton added the bug Something isn't working label Feb 22, 2023
@ktmeaton ktmeaton added this to the v0.7.0 milestone Feb 22, 2023
This was referenced Feb 22, 2023
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