Merge pull request #23 from nextstrain/vaccine-strains

Include vaccine strains

ingest/defaults/annotations.tsv

@@ -4,3 +4,23 @@
 # If there are multiple annotations for the same id and field, then the last value is used
 # Lines starting with '#' are treated as comments
 # Any '#' after the field value are treated as comments.
+#
+# Vaccine strain information from Parks et al. Comparison of predicted amino acid
+# sequences of measles virus strains in the Edmonston vaccine lineage
+# https://doi.org/10.1128/jvi.75.2.910-920.2001
+AF266288.2	strain	Measles strain Edmonston WT
+AF266288.2	date	1954
+AF266288.2	region	North America
+AF266288.2	country	USA
+AF266288.2	division	Massachusetts
+AF266288.2	location	Boston
+AF266287.1	strain	Measles vaccine strain Moraten
+AF266287.1	date	1954
+AF266290.1	strain	Measles vaccine strain Zagreb
+AF266290.1	date	1954
+AF266289.1	strain	Measles vaccine strain Rubeovax
+AF266289.1	date	1954
+AF266291.1	strain	Measles vaccine strain Schwarz
+AF266291.1	date	1954
+AF266286.1	strain	Measles vaccine strain AIK-C
+AF266286.1	date	1954

phylogenetic/defaults/config.yaml

@@ -7,8 +7,8 @@ files:
     colors: "defaults/colors.tsv"
     auspice_config: "defaults/auspice_config.json"
     auspice_config_N450: "defaults/auspice_config_N450.json"
-filter: 
-    group_by: "country year month"
+filter:
+    group_by: "country year"
     sequences_per_group: 20
     min_date: 1950
     min_length: 5000
@@ -20,6 +20,8 @@ filter_N450:
 refine:
     coalescent: "opt"
     date_inference: "marginal"
-    clock_filter_iqd: 4  
+    clock_filter_iqd: 4
 ancestral:
     inference: "joint"
+export:
+    metadata_columns: "strain division location"

phylogenetic/rules/export.smk

@@ -15,11 +15,11 @@ rule export:
         aa_muts = "results/{gene}/aa_muts.json",
         colors = config["files"]["colors"],
         auspice_config = lambda wildcard: "defaults/auspice_config.json" if wildcard.gene in ["genome"] else "defaults/auspice_config_N450.json"
-
     output:
         auspice_json = "auspice/measles_{gene}.json"
     params:
-        strain_id = config["strain_id_field"]
+        strain_id = config["strain_id_field"],
+        metadata_columns = config["export"]["metadata_columns"]
     shell:
         """
         augur export v2 \
@@ -28,6 +28,7 @@ rule export:
             --metadata-id-columns {params.strain_id} \
             --node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} \
             --colors {input.colors} \
+            --metadata-columns {params.metadata_columns} \
             --auspice-config {input.auspice_config} \
             --include-root-sequence-inline \
             --output {output.auspice_json}