Merge pull request #12 from nextstrain/james/year

Add sampling year coloring
nextstrain · Aug 22, 2024 · 1df5993 · 1df5993
2 parents 67b7941 + 0534d0d
commit 1df5993
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Showing 3 changed files with 24 additions and 2 deletions.
diff --git a/phylogenetic/defaults/auspice_config.json b/phylogenetic/defaults/auspice_config.json
@@ -27,6 +27,11 @@
       "title": "Country",
       "type": "categorical"
     },
+    {
+      "key": "year",
+      "title": "Sampling year",
+      "type": "continuous"
+    },
     {
       "key": "host",
       "title": "Host",
@@ -60,6 +65,7 @@
     "author",
     "strain",
     "division",
-    "location"
+    "location",
+    "date"
   ]
 }
diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk
@@ -51,3 +51,18 @@ rule translate:
             --output {output.node_data} \
             2>&1 | tee {log}
         """
+
+rule add_year_metadata:
+    input:
+        metadata = "data/metadata.tsv",
+    params:
+        strain_id = config["strain_id_field"],
+    output:
+        node_data = "results/year.json"
+    run:
+        from augur.io import read_metadata
+        import json
+        m = read_metadata(input.metadata, id_columns=[params.strain_id])
+        nodes = {name: {'year': date.split('-')[0]} for name,date in zip(m.index, m['date']) if date and not date.startswith('X')}
+        with open(output.node_data, 'w') as fh:
+            json.dump({"nodes": nodes}, fh)
diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
@@ -13,6 +13,7 @@ rule export:
         branch_lengths = "results/branch_lengths.json",
         nt_muts = "results/nt_muts.json",
         aa_muts = "results/aa_muts.json",
+        year = "results/year.json",
         colors = config["files"]["colors"],
         auspice_config = config["files"]["auspice_config"],
         description = config["files"]["description"]
@@ -30,7 +31,7 @@ rule export:
             --tree {input.tree} \
             --metadata {input.metadata} \
             --metadata-id-columns {params.strain_id} \
-            --node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} \
+            --node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} {input.year} \
             --colors {input.colors} \
             --auspice-config {input.auspice_config} \
             --include-root-sequence-inline \