Add frequencies panels

nextstrain · Dec 20, 2024 · 65520e5 · 65520e5
1 parent 4acba65
commit 65520e5
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diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
@@ -10,6 +10,7 @@ wildcard_constraints:
 rule all:
     input:
         auspice_json = expand("auspice/dengue_{serotype}_{gene}.json", serotype=serotypes, gene=genes),
+        tip_frequencies_json= expand("auspice/dengue_{serotype}_{gene}_tip-frequencies.json", serotype=serotypes, gene=genes)
 
 include: "rules/prepare_sequences.smk"
 include: "rules/prepare_sequences_E.smk"

diff --git a/phylogenetic/defaults/config_dengue.yaml b/phylogenetic/defaults/config_dengue.yaml
@@ -38,5 +38,11 @@ clades:
     denv3: 'defaults/clades_genotypes.tsv'
     denv4: 'defaults/clades_genotypes.tsv'
 
+tip_frequencies:
+    min_date: "1980-01-01"
+    max_date: "6M"
+    narrow_bandwidth: 0.2
+    wide_bandwidth: 0.6
+
 export:
   description: "defaults/description.md"
diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
@@ -102,6 +102,12 @@ rule prepare_auspice_config:
               "region",
               "author"
             ],
+            "panels": [
+              "tree",
+              "map",
+              "entropy",
+              "frequencies"
+            ],
             "metadata_columns": [
               "accession",
               "url"
@@ -179,3 +185,32 @@ rule final_strain_name:
             --display-strain-name {params.display_strain_field} \
             --output {output.auspice_json}
         """
+
+rule tip_frequencies:
+    """
+    Estimating KDE frequencies for tips
+    """
+    input:
+        tree = "results/{gene}/tree_{serotype}.nwk",
+        metadata = "data/metadata_{serotype}.tsv",
+    output:
+        tip_freq = "auspice/dengue_{serotype}_{gene}_tip-frequencies.json"
+    params:
+        strain_id = config["strain_id_field"],
+        min_date = config["tip_frequencies"]["min_date"],
+        max_date = config["tip_frequencies"]["max_date"],
+        narrow_bandwidth = config["tip_frequencies"]["narrow_bandwidth"],
+        wide_bandwidth = config["tip_frequencies"]["wide_bandwidth"]
+    shell:
+        r"""
+        augur frequencies \
+            --method kde \
+            --tree {input.tree} \
+            --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
+            --min-date {params.min_date} \
+            --max-date {params.max_date} \
+            --narrow-bandwidth {params.narrow_bandwidth} \
+            --wide-bandwidth {params.wide_bandwidth} \
+            --output {output.tip_freq}
+        """