diff --git a/nextclade/config/auspice_config.json b/nextclade/config/auspice_config.json index 8d0e215..28d1af3 100644 --- a/nextclade/config/auspice_config.json +++ b/nextclade/config/auspice_config.json @@ -25,7 +25,7 @@ "type": "categorical" }, { - "key": "proposed_clade", + "key": "proposed_subclade", "title": "Subclade proposals", "type": "categorical" }, diff --git a/nextclade/config/config_dict.yaml b/nextclade/config/config_dict.yaml index d0a8e0c..ccf9451 100644 --- a/nextclade/config/config_dict.yaml +++ b/nextclade/config/config_dict.yaml @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" @@ -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" diff --git a/nextclade/dataset_config/h1n1pdm/includes.txt b/nextclade/dataset_config/h1n1pdm/includes.txt index 42047c0..4f7d96b 100644 --- a/nextclade/dataset_config/h1n1pdm/includes.txt +++ b/nextclade/dataset_config/h1n1pdm/includes.txt @@ -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 diff --git a/nextclade/scripts/merge_jsons.py b/nextclade/scripts/merge_jsons.py index cf8da62..d1bf586 100644 --- a/nextclade/scripts/merge_jsons.py +++ b/nextclade/scripts/merge_jsons.py @@ -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__": @@ -73,4 +72,3 @@ def get_clade_configs(name): with open(args.output_auspice, 'w') as fh: json.dump(auspice_json, fh, indent=2) -