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cov-lineages / pangolin-data

Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
GNU General Public License v3.0
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Alias XDS missing #52

Open WhalleyT opened 7 months ago

WhalleyT commented 7 months ago

Hi,

I noticed when running pangolin that the alias keys don't seem to be updated from 1.24 -> 1.25. When running pangolin I get the error

generate_final_report(preprocessing_csv, inference_csv, cached_csv, config[KEY_ALIAS_FILE], constellation_list, config[KEY_PANGOLIN_DATA_VERSION],config[KEY_ANALYSIS_MODE], args.skip_designation_cache, config[KEY_OUTFILE],config)
  File "/lib/python3.8/site-packages/pangolin/utils/report_collation.py", line 234, in generate_final_report
    recombinant_parents = get_recombinant_parents(expanded_pango_lineage, alias_dict)
  File "/lib/python3.8/site-packages/pangolin/utils/report_collation.py", line 94, in get_recombinant_parents
    for parent in alias_dict[lineage_parts[0]]:
KeyError: 'XDS

and I see that in pangolin_data/data/alias_key.json XDS is not there in spite of having been added into pango-designation and it looks like the json is still at 1.24 where the remaining files are at 1.25. Sorry if I'm getting the wrong end of the stick or the files are still in the process of being bumped up!

Thanks, Tom

AngieHinrichs commented 7 months ago

No, you're right Tom! I accidentally checked out the wrong version of pango-designation when copying in that file. Fixed so it won't happen that way in the future. Stand by for a v1.25.1, sorry about that.

AngieHinrichs commented 7 months ago

pangolin-data v1.25.1 is out now. Thanks so much for reporting this @WhalleyT!

WhalleyT commented 7 months ago

That's great! Thanks for the speedy update 🙂