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Refine proposed subclades in Nextclade datasets #194

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2 changes: 1 addition & 1 deletion nextclade/config/auspice_config.json
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
"type": "categorical"
},
{
"key": "proposed_clade",
"key": "proposed_subclade",
"title": "Subclade proposals",
"type": "categorical"
},
Expand Down
24 changes: 12 additions & 12 deletions nextclade/config/config_dict.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,9 @@ builds:
subclade:
url: "seasonal_A-H1N1pdm_HA/main/.auto-generated/subclades.tsv"
key: "subclade"
proposed_clade:
proposed_subclade:
url: "seasonal_A-H1N1pdm_HA/main/.auto-generated/subclade_proposals.tsv"
key: "proposed_clade"
key: "proposed_subclade"
refs:
CY121680: # exclude South Korean genomes because of sequencing artifacts close to the start of HA
filter: "--min-date 2009 --probabilistic-sampling --exclude-where country='south_korea' qc.overallStatus='bad' --group-by year --min-length 1500 --subsample-max-sequences 1500"
Expand All @@ -35,9 +35,9 @@ builds:
clade_systems:
clade:
url: "seasonal_A-H1N1pdm_NA/main/.auto-generated/subclades.tsv"
proposed_clade:
proposed_subclade:
url: "seasonal_A-H1N1pdm_NA/main/.auto-generated/subclade_proposals.tsv"
key: "proposed_clade"
key: "proposed_subclade"
refs:
MW626056:
filter: "--min-date 2019 --probabilistic-sampling --group-by year region --min-length 1400 --subsample-max-sequences 2000"
Expand All @@ -57,9 +57,9 @@ builds:
short-clade:
url: "seasonal_A-H3N2_HA/main/.auto-generated/clades.tsv"
key: "short-clade"
proposed_clade:
proposed_subclade:
url: "seasonal_A-H3N2_HA/main/.auto-generated/subclade_proposals.tsv"
key: "proposed_clade"
key: "proposed_subclade"
refs:
EPI1857216:
filter: "--min-date 2019 --probabilistic-sampling --group-by year region --min-length 1500 --subsample-max-sequences 2000"
Expand All @@ -78,9 +78,9 @@ builds:
clade_systems:
clade:
url: "seasonal_A-H3N2_NA/main/.auto-generated/subclades.tsv"
proposed_clade:
proposed_subclade:
url: "seasonal_A-H3N2_NA/main/.auto-generated/subclade_proposals.tsv"
key: "proposed_clade"
key: "proposed_subclade"
refs:
EPI1857215:
filter: "--min-date 2019 --probabilistic-sampling --group-by year region --min-length 1400 --subsample-max-sequences 1500"
Expand All @@ -97,9 +97,9 @@ builds:
subclade:
url: "seasonal_B-Vic_HA/main/.auto-generated/subclades.tsv"
key: "subclade"
proposed_clade:
proposed_subclade:
url: "seasonal_B-Vic_HA/main/.auto-generated/subclade_proposals.tsv"
key: "proposed_clade"
key: "proposed_subclade"
refs:
KX058884:
filter: "--min-date 2014 --probabilistic-sampling --group-by year --min-length 1500 --subsample-max-sequences 2000"
Expand All @@ -112,9 +112,9 @@ builds:
clade_systems:
clade:
url: "seasonal_B-Vic_NA/main/.auto-generated/subclades.tsv"
proposed_clade:
proposed_subclade:
url: "seasonal_B-Vic_NA/main/.auto-generated/subclade_proposals.tsv"
key: "proposed_clade"
key: "proposed_subclade"
refs:
CY073894:
filter: "--min-date 2014 --probabilistic-sampling --group-by year region --min-length 1400 --subsample-max-sequences 2000"
Expand Down
1 change: 1 addition & 0 deletions nextclade/dataset_config/h1n1pdm/includes.txt
Original file line number Diff line number Diff line change
Expand Up @@ -59,3 +59,4 @@ A/Helsinki/2430/2012
A/Gansu-Ganzhou/SWL34/2012
A/Brisbane/96/2012
A/Minnesota/23/2014
A/Nagano/2649/2018
6 changes: 2 additions & 4 deletions nextclade/scripts/merge_jsons.py
Original file line number Diff line number Diff line change
Expand Up @@ -18,13 +18,12 @@ def get_clade_configs(name):
"displayName": "Subclade",
"description": "Experimental fine-grained subclade annotation."
},
"proposed_clade": {
"proposed_subclade": {
"name": "Subclade proposal",
"displayName": "Subclade proposal",
"description": "Includes proposals of new subclades. These can change anytime.",
"hideInWeb": True
}
}.get(name, {'name':name, "displayName":name, "description":""})
}}.get(name, {'name':name, "displayName":name, "description":""})


if __name__=="__main__":
Expand Down Expand Up @@ -73,4 +72,3 @@ def get_clade_configs(name):

with open(args.output_auspice, 'w') as fh:
json.dump(auspice_json, fh, indent=2)