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nextstrain · Aug 1, 2023 · dd4e54e · dd4e54e
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Showing 60 changed files with 234 additions and 83 deletions.
diff --git a/README.md b/README.md
diff --git a/clade-labeling/add-clades.py b/clade-labeling/add-clades.py
diff --git a/clade-labeling/update-clades.py b/clade-labeling/update-clades.py
@@ -84,7 +84,7 @@ def append_new_clades(new_clades, old_clades):
 
 """run label and reformat the output"""
 print("\nrunning LABEL to assign clades to", len(new_strains), "new strains of", subtype)
-os.system('flu-amd/LABEL -D {new_strains_fasta} {label_output} H5v2015'.format(new_strains_fasta=new_strains_fasta, label_output=label_output))
+os.system('flu-amd/./LABEL -D {new_strains_fasta} {label_output} H5v2015'.format(new_strains_fasta=new_strains_fasta, label_output=label_output))
 os.system('python clade-labeling/check-LABEL-annotations.py --label_output {label_output}_final.txt --output {new_clades_file}'.format(new_clades_file=new_clades_file, label_output=label_output))
 
 

diff --git a/config/auspice_config_h5n1.json b/config/auspice_config_h5n1.json
@@ -1,78 +1,108 @@
-{
-  "title": "Real-time tracking of influenza A/H5N1 virus evolution",
-  "maintainers": [
-    {"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"}
-  ],
-  "build_url": "https://github.com/nextstrain/avian-flu",
-  "data_provenance": [
-    {
-      "name": "GISAID"
-    }
-  ],
-  "colorings": [
-    {
-      "key": "gt",
-      "title": "Genotype",
-      "type": "categorical"
-    },
-    {
-      "key": "num_date",
-      "title": "Date",
-      "type": "continuous"
-    },
-    {
-      "key": "country",
-      "title": "Country",
-      "type": "categorical"
-    },
-    {
-      "key": "region",
-      "title": "Region",
-      "type": "categorical"
-    },
-    {
-      "key": "host",
-      "title": "Host",
-      "type": "categorical"
-    },
-    {
-      "key": "domestic_status",
-      "title": "Domestic or Wild",
-      "type": "categorical"
-    },
-    {
-      "key": "h5_label_clade",
-      "title": "H5 clade",
-      "type": "categorical"
-    },
-    {
-      "key": "furin_cleavage_motif",
-      "title": "furin cleavage motif",
-      "type": "categorical"
-    },
-    {
-      "key": "cleavage_site_sequence",
-      "title": "cleavage site sequence",
-      "type": "categorical"
-    },
-    {
-      "key": "submitting_lab",
-      "title": "Submitting lab",
-      "type": "categorical"
-    }
-  ],
-  "geo_resolutions": [
-    "region",
-    "country"
-  ],
-  "display_defaults": {
-    "map_triplicate": true,
-    "color_by": "region"
-  },
-  "filters": [
-    "host",
-    "region",
-    "country",
-    "submitting_lab"
-  ]
-}
+{
+  "title": "Real-time tracking of influenza A/H5N1 virus evolution",
+  "maintainers": [
+    {"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"}
+  ],
+  "build_url": "https://github.com/nextstrain/avian-flu",
+  "data_provenance": [
+    {
+      "name": "GISAID"
+    }
+  ],
+  "colorings": [
+    {
+      "key": "gt",
+      "title": "Genotype",
+      "type": "categorical"
+    },
+    {
+      "key": "num_date",
+      "title": "Date",
+      "type": "continuous"
+    },
+    {
+      "key": "country",
+      "title": "Country",
+      "type": "categorical"
+    },
+    {
+      "key": "region",
+      "title": "Region",
+      "type": "categorical"
+    },
+    {
+      "key": "host",
+      "title": "Host",
+      "type": "categorical"
+    },
+    {
+      "key": "domestic_status",
+      "title": "Domestic or Wild",
+      "type": "categorical"
+    },
+    {
+      "key": "subtype",
+      "title": "Subtype",
+      "type": "categorical"
+    },
+    {
+      "key": "h5_label_clade",
+      "title": "LABEL clade",
+      "type": "categorical"
+    },
+    {
+      "key": "gisaid_clade",
+      "title": "GISAID clade",
+      "type": "categorical"
+    },
+    {
+      "key": "furin_cleavage_motif",
+      "title": "furin cleavage motif",
+      "type": "categorical"
+    },
+    {
+      "key": "cleavage_site_sequence",
+      "title": "cleavage site sequence",
+      "type": "categorical"
+    },
+    {
+      "key": "authors",
+      "title": "Authors",
+      "type": "categorical"
+    },
+    {
+      "key": "PMID",
+      "title": "Pubmed ID",
+      "type": "categorical"
+    },
+    {
+      "key": "submitting_lab",
+      "title": "Submitting lab",
+      "type": "categorical"
+    },
+    {
+      "key": "originating_lab",
+      "title": "Originating lab",
+      "type": "categorical"
+    }
+  ],
+  "geo_resolutions": [
+    "region",
+    "country"
+  ],
+  "display_defaults": {
+    "map_triplicate": true,
+    "color_by": "region"
+  },
+  "filters": [
+    "host",
+    "domestic_status",
+    "region",
+    "country",
+    "submitting_lab",
+    "subtype",
+    "h5_label_clade",
+    "gisaid_clade",
+    "authors"
+  ]
+}
diff --git a/config/auspice_config_h5nx.json b/config/auspice_config_h5nx.json
@@ -47,7 +47,12 @@
     },
     {
       "key": "h5_label_clade",
-      "title": "H5 clade",
+      "title": "LABEL clade",
+      "type": "categorical"
+    },
+    {
+      "key": "gisaid_clade",
+      "title": "GISAID clade",
       "type": "categorical"
     },
     {
@@ -60,6 +65,16 @@
       "title": "cleavage site sequence",
       "type": "categorical"
     },
+    {
+      "key": "authors",
+      "title": "Authors",
+      "type": "categorical"
+    },
+    {
+      "key": "PMID",
+      "title": "Pubmed ID",
+      "type": "categorical"
+    },
     {
       "key": "submitting_lab",
       "title": "Submitting lab",
@@ -81,10 +96,13 @@
   },
   "filters": [
     "host",
+    "domestic_status",
     "region",
     "country",
     "submitting_lab",
     "subtype",
-    "h5_label_clade"
+    "h5_label_clade",
+    "gisaid_clade",
+    "authors"
   ]
 }
diff --git a/config/auspice_config_h7n9.json b/config/auspice_config_h7n9.json
diff --git a/config/auspice_config_h9n2.json b/config/auspice_config_h9n2.json
diff --git a/config/colors_h5n1.tsv b/config/colors_h5n1.tsv
@@ -53,4 +53,56 @@ h5_label_clade	8	#E2592C
 h5_label_clade	8-9-like	#E04D29
 h5_label_clade	9	#DF4127
 h5_label_clade	EA-nonGsGD	#DD3425
-h5_label_clade	Am-nonGsGD	#891916
+h5_label_clade	Am-nonGsGD	#891916
+gisaid_clade	0	#5E1D9D
+gisaid_clade	1	#521EA7
+gisaid_clade	1-8-9-like	#4C24B0
+gisaid_clade	1.1	#472DB8
+gisaid_clade	1.1-like	#4335C0
+gisaid_clade	1.1.1	#403EC6
+gisaid_clade	1.1.2	#3F48C9
+gisaid_clade	2.1.1	#3F53CD
+gisaid_clade	2.1.2	#3E5DD0
+gisaid_clade	2.1.3	#4066CF
+gisaid_clade	2.1.3.1	#4270CE
+gisaid_clade	2.1.3.2	#4379CD
+gisaid_clade	2.1.3.2a	#4682C9
+gisaid_clade	2.1.3.2b	#4989C4
+gisaid_clade	2.1.3.3	#4C91C0
+gisaid_clade	2.2	#5097BA
+gisaid_clade	2.2.1	#549DB3
+gisaid_clade	2.2.1.1	#58A2AC
+gisaid_clade	2.2.1.1a	#5CA7A5
+gisaid_clade	2.2.1.2	#61AB9D
+gisaid_clade	2.2.2	#67AE95
+gisaid_clade	2.2.2.1	#6CB28D
+gisaid_clade	2.3.1	#72B485
+gisaid_clade	2.3.2	#78B77D
+gisaid_clade	2.3.2.1	#7FB976
+gisaid_clade	2.3.2.1a	#85BA6E
+gisaid_clade	2.3.2.1b	#8CBB68
+gisaid_clade	2.3.2.1c	#93BD62
+gisaid_clade	2.3.3	#9BBE5C
+gisaid_clade	2.3.4	#A2BE57
+gisaid_clade	2.3.4-like	#A9BD53
+gisaid_clade	2.3.4.1	#B1BD4E
+gisaid_clade	2.3.4.2	#B8BC4B
+gisaid_clade	2.3.4.3	#BFBB48
+gisaid_clade	2.3.4.4	#C5B945
+gisaid_clade	2.3.4.4b	#CCB742
+gisaid_clade	2.3.4.4c	#D1B340
+gisaid_clade	2.3.4.4g	#D6AF3E
+gisaid_clade	2.3.4.4e	#DCAB3D
+gisaid_clade	2.3.4.4h	#DFA53B
+gisaid_clade	2.5	#E29E39
+gisaid_clade	3	#E49838
+gisaid_clade	4	#E68F36
+gisaid_clade	5	#E68634
+gisaid_clade	6	#E67C33
+gisaid_clade	7	#E67231
+gisaid_clade	7.1	#E4652E
+gisaid_clade	7.2	#E2592C
+gisaid_clade	8	#E04D29
+gisaid_clade	9	#DF4127
+gisaid_clade	EA_nonGsGD	#DD3425
+gisaid_clade	Am_nonGsGD	#891916
diff --git a/config/colors_h5nx.tsv b/config/colors_h5nx.tsv
@@ -63,4 +63,55 @@ h5_label_clade	8-9-like	#E04D29
 h5_label_clade	9	#DF4127
 h5_label_clade	EA-nonGsGD	#DD3425
 h5_label_clade	Am-nonGsGD	#891916
-
+gisaid_clade	0	#5E1D9D
+gisaid_clade	1	#521EA7
+gisaid_clade	1-8-9-like	#4C24B0
+gisaid_clade	1.1	#472DB8
+gisaid_clade	1.1-like	#4335C0
+gisaid_clade	1.1.1	#403EC6
+gisaid_clade	1.1.2	#3F48C9
+gisaid_clade	2.1.1	#3F53CD
+gisaid_clade	2.1.2	#3E5DD0
+gisaid_clade	2.1.3	#4066CF
+gisaid_clade	2.1.3.1	#4270CE
+gisaid_clade	2.1.3.2	#4379CD
+gisaid_clade	2.1.3.2a	#4682C9
+gisaid_clade	2.1.3.2b	#4989C4
+gisaid_clade	2.1.3.3	#4C91C0
+gisaid_clade	2.2	#5097BA
+gisaid_clade	2.2.1	#549DB3
+gisaid_clade	2.2.1.1	#58A2AC
+gisaid_clade	2.2.1.1a	#5CA7A5
+gisaid_clade	2.2.1.2	#61AB9D
+gisaid_clade	2.2.2	#67AE95
+gisaid_clade	2.2.2.1	#6CB28D
+gisaid_clade	2.3.1	#72B485
+gisaid_clade	2.3.2	#78B77D
+gisaid_clade	2.3.2.1	#7FB976
+gisaid_clade	2.3.2.1a	#85BA6E
+gisaid_clade	2.3.2.1b	#8CBB68
+gisaid_clade	2.3.2.1c	#93BD62
+gisaid_clade	2.3.3	#9BBE5C
+gisaid_clade	2.3.4	#A2BE57
+gisaid_clade	2.3.4-like	#A9BD53
+gisaid_clade	2.3.4.1	#B1BD4E
+gisaid_clade	2.3.4.2	#B8BC4B
+gisaid_clade	2.3.4.3	#BFBB48
+gisaid_clade	2.3.4.4	#C5B945
+gisaid_clade	2.3.4.4b	#CCB742
+gisaid_clade	2.3.4.4c	#D1B340
+gisaid_clade	2.3.4.4g	#D6AF3E
+gisaid_clade	2.3.4.4e	#DCAB3D
+gisaid_clade	2.3.4.4h	#DFA53B
+gisaid_clade	2.5	#E29E39
+gisaid_clade	3	#E49838
+gisaid_clade	4	#E68F36
+gisaid_clade	5	#E68634
+gisaid_clade	6	#E67C33
+gisaid_clade	7	#E67231
+gisaid_clade	7.1	#E4652E
+gisaid_clade	7.2	#E2592C
+gisaid_clade	8	#E04D29
+gisaid_clade	9	#DF4127
+gisaid_clade	EA_nonGsGD	#DD3425
+gisaid_clade	Am_nonGsGD	#891916
diff --git a/config/colors_h7n9.tsv b/config/colors_h7n9.tsv
diff --git a/config/colors_h9n2.tsv b/config/colors_h9n2.tsv
diff --git a/config/dropped_strains_h5n1.txt b/config/dropped_strains_h5n1.txt
diff --git a/config/dropped_strains_h5nx.txt b/config/dropped_strains_h5nx.txt
diff --git a/config/dropped_strains_h7n9.txt b/config/dropped_strains_h7n9.txt
diff --git a/config/dropped_strains_h9n2.txt b/config/dropped_strains_h9n2.txt
diff --git a/config/lat_longs_h5n1.tsv b/config/lat_longs_h5n1.tsv
diff --git a/config/lat_longs_h5nx.tsv b/config/lat_longs_h5nx.tsv
diff --git a/config/lat_longs_h7n9.tsv b/config/lat_longs_h7n9.tsv
diff --git a/config/lat_longs_h9n2.tsv b/config/lat_longs_h9n2.tsv
diff --git a/config/reference_h5n1_ha.gb b/config/reference_h5n1_ha.gb
diff --git a/config/reference_h5n1_mp.gb b/config/reference_h5n1_mp.gb
diff --git a/config/reference_h5n1_na.gb b/config/reference_h5n1_na.gb
diff --git a/config/reference_h5n1_np.gb b/config/reference_h5n1_np.gb
diff --git a/config/reference_h5n1_ns.gb b/config/reference_h5n1_ns.gb
diff --git a/config/reference_h5n1_pa.gb b/config/reference_h5n1_pa.gb
diff --git a/config/reference_h5n1_pb1.gb b/config/reference_h5n1_pb1.gb
diff --git a/config/reference_h5n1_pb2.gb b/config/reference_h5n1_pb2.gb
diff --git a/config/reference_h5nx_ha.gb b/config/reference_h5nx_ha.gb
diff --git a/config/reference_h5nx_mp.gb b/config/reference_h5nx_mp.gb
diff --git a/config/reference_h5nx_na.gb b/config/reference_h5nx_na.gb
diff --git a/config/reference_h5nx_np.gb b/config/reference_h5nx_np.gb
diff --git a/config/reference_h5nx_ns.gb b/config/reference_h5nx_ns.gb
diff --git a/config/reference_h5nx_pa.gb b/config/reference_h5nx_pa.gb
diff --git a/config/reference_h5nx_pb1.gb b/config/reference_h5nx_pb1.gb
diff --git a/config/reference_h5nx_pb2.gb b/config/reference_h5nx_pb2.gb
diff --git a/config/reference_h7n9_ha.gb b/config/reference_h7n9_ha.gb
diff --git a/config/reference_h7n9_mp.gb b/config/reference_h7n9_mp.gb
diff --git a/config/reference_h7n9_na.gb b/config/reference_h7n9_na.gb
diff --git a/config/reference_h7n9_np.gb b/config/reference_h7n9_np.gb
diff --git a/config/reference_h7n9_ns.gb b/config/reference_h7n9_ns.gb
diff --git a/config/reference_h7n9_pa.gb b/config/reference_h7n9_pa.gb
diff --git a/config/reference_h7n9_pb1.gb b/config/reference_h7n9_pb1.gb
diff --git a/config/reference_h7n9_pb2.gb b/config/reference_h7n9_pb2.gb
diff --git a/config/reference_h9n2_ha.gb b/config/reference_h9n2_ha.gb
diff --git a/config/reference_h9n2_mp.gb b/config/reference_h9n2_mp.gb
diff --git a/config/reference_h9n2_na.gb b/config/reference_h9n2_na.gb
diff --git a/config/reference_h9n2_np.gb b/config/reference_h9n2_np.gb
diff --git a/config/reference_h9n2_ns.gb b/config/reference_h9n2_ns.gb
diff --git a/config/reference_h9n2_pa.gb b/config/reference_h9n2_pa.gb
diff --git a/config/reference_h9n2_pb1.gb b/config/reference_h9n2_pb1.gb
diff --git a/config/reference_h9n2_pb2.gb b/config/reference_h9n2_pb2.gb
diff --git a/example_data/h5n1_ha.fasta b/example_data/h5n1_ha.fasta
diff --git a/quickstart-build/config/auspice_config_h5n1.json b/quickstart-build/config/auspice_config_h5n1.json
diff --git a/quickstart-build/config/dropped_strains_h5n1.txt b/quickstart-build/config/dropped_strains_h5n1.txt
diff --git a/quickstart-build/config/include_strains_h5n1.txt b/quickstart-build/config/include_strains_h5n1.txt
diff --git a/quickstart-build/config/reference_h5n1_ha.gb b/quickstart-build/config/reference_h5n1_ha.gb
diff --git a/quickstart-build/images/build-results-tree.png b/quickstart-build/images/build-results-tree.png
diff --git a/quickstart-build/images/build-results.png b/quickstart-build/images/build-results.png
diff --git a/quickstart-build/images/check-setup-output.png b/quickstart-build/images/check-setup-output.png
diff --git a/scripts/annotate-ha-cleavage-site.py b/scripts/annotate-ha-cleavage-site.py