Merge pull request #22 from nextstrain/french-guiana-latlong

Plot French Guiana samples by geography
nextstrain · Jan 13, 2025 · 7c12cef · 7c12cef
2 parents 219e638 + 01c52d1
commit 7c12cef
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diff --git a/ingest/defaults/geolocation_rules.tsv b/ingest/defaults/geolocation_rules.tsv
@@ -4,3 +4,6 @@
 # If creating a general rule, then the raw field value can be substituted with '*'
 # Lines starting with '#' will be ignored as comments.
 # Trailing '#' will be ignored as comments.
+Europe/France/French Guiana/*	South America/French Guiana (France)/French Guiana (France)/*
+Europe/France/France Guiana/*	South America/French Guiana (France)/French Guiana (France)/*
+South America/French Guiana/*/*	South America/French Guiana (France)/*/*
diff --git a/phylogenetic/defaults/config.yaml b/phylogenetic/defaults/config.yaml
@@ -3,6 +3,7 @@ files:
     exclude: "defaults/dropped_strains.txt"
     reference: "defaults/rabies_reference.gb"
     colors: "defaults/colors.tsv"
+    lat_longs: "defaults/lat_longs.tsv"
     auspice_config: "defaults/auspice_config.json"
     description: "defaults/description.md"
     clades: "defaults/clades.tsv"

diff --git a/phylogenetic/defaults/lat_longs.tsv b/phylogenetic/defaults/lat_longs.tsv
@@ -0,0 +1 @@
+country	French Guiana (France)	4.0039882	-52.999998
diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
@@ -16,6 +16,7 @@ rule export:
         clades = "results/clades.json",
         year = "results/year.json",
         colors = config["files"]["colors"],
+        lat_longs = config["files"]["lat_longs"],
         auspice_config = config["files"]["auspice_config"],
         description = config["files"]["description"]
     output:
@@ -34,6 +35,7 @@ rule export:
             --metadata-id-columns {params.strain_id} \
             --node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} {input.year} {input.clades} \
             --colors {input.colors} \
+            --lat-longs {input.lat_longs} \
             --auspice-config {input.auspice_config} \
             --include-root-sequence-inline \
             --output {output.auspice_json} \
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		country French Guiana (France) 4.0039882 -52.999998