updating clades, adding human Missouri sequence to include files

nextstrain · Sep 17, 2024 · 97de0b4 · 97de0b4
1 parent 0ddee36
commit 97de0b4
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Showing 9 changed files with 1,718 additions and 10 deletions.
diff --git a/Snakefile.clades b/Snakefile.clades
@@ -1,19 +1,17 @@
-include: "Snakefile"
-
 
 rule update_clades:
     message: "Finding new h5n1 strains and annotating their clades with LABEL"
     shell:
         """
         python clade-labeling/update-clades.py \
-            --metadata data/metadata_h5n1.tsv \
-            --sequences data/sequences_h5n1_ha.fasta \
+            --metadata results/h5n1/metadata.tsv \
+            --sequences results/h5n1/ha/sequences.fasta \
             --clades_file clade-labeling/h5n1-clades.tsv \
             --subtype h5n1 \
 
         python clade-labeling/update-clades.py \
-            --metadata data/metadata_h5nx.tsv \
-            --sequences data/sequences_h5nx_ha.fasta \
+            --metadata results/h5nx/metadata.tsv \
+            --sequences results/h5nx/ha/sequences.fasta \
             --clades_file clade-labeling/h5nx-clades.tsv \
             --subtype h5nx
         """
diff --git a/clade-labeling/h5n1-clades.tsv b/clade-labeling/h5n1-clades.tsv
diff --git a/clade-labeling/h5nx-clades.tsv b/clade-labeling/h5nx-clades.tsv
diff --git a/config/h5n1/dropped_strains_h5n1.txt b/config/h5n1/dropped_strains_h5n1.txt
@@ -13,6 +13,7 @@ A/egret/Korea/22WC603/2023
 A/chicken/Poland/003/2020
 A/chicken/Scotland/128320/2023
 A/Tuftedduck/Netherlands/1/2023
+A/teal/Nuble/2335162/2023
 
 
 # Duplicated entries in GISAID

diff --git a/config/h5n1/include_strains_h5n1_2y.txt b/config/h5n1/include_strains_h5n1_2y.txt
@@ -327,4 +327,5 @@ A/turkey/Wisconsin/24000378002original/2024
 A/turkey/Wisconsin/24000378003original/2024
 A/turkeyvulture/California/24007419001/2024
 A/westerngull/California/24004708001/2024
-A/woodduck/Mississippi/24004235001/2024
+A/woodduck/Mississippi/24004235001/2024
+A/Missouri/121/2024
diff --git a/config/h5n1/include_strains_h5n1_all-time.txt b/config/h5n1/include_strains_h5n1_all-time.txt
@@ -36,4 +36,5 @@ A/feline/USA/24009311006original/2024
 A/feline/USA/24008764002original/2024
 A/feline/USA/23037332001original/2023
 A/feline/USA/24008850002original/2024
-A/feline/USA/24009311004original/2024
+A/feline/USA/24009311004original/2024
+A/Missouri/121/2024
diff --git a/config/h5nx/dropped_strains_h5nx.txt b/config/h5nx/dropped_strains_h5nx.txt
@@ -28,7 +28,7 @@ A/egret/Korea/22WC603/2023
 A/chicken/Poland/003/2020
 A/chicken/Scotland/128320/2023
 A/Tuftedduck/Netherlands/1/2023
-
+A/teal/Nuble/2335162/2023
 
 
 # Duplicated entries in GISAID

diff --git a/config/h5nx/include_strains_h5nx_2y.txt b/config/h5nx/include_strains_h5nx_2y.txt
@@ -329,3 +329,4 @@ A/turkey/Wisconsin/24000378003original/2024
 A/turkeyvulture/California/24007419001/2024
 A/westerngull/California/24004708001/2024
 A/woodduck/Mississippi/24004235001/2024
+A/Missouri/121/2024
diff --git a/config/h5nx/include_strains_h5nx_all-time.txt b/config/h5nx/include_strains_h5nx_all-time.txt
@@ -26,4 +26,5 @@ A/goat/Minnesota/24007234006original/2024
 A/goat/Minnesota/24007234009original/2024
 A/goat/Minnesota/24007234003original/2024
 A/Texas/37/2024
-A/StateofMexico/INERINF645/2024
+A/StateofMexico/INERINF645/2024
+A/Missouri/121/2024