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Plot French Guiana samples by geography #22

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merged 2 commits into from
Jan 13, 2025
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Merged

Plot French Guiana samples by geography #22

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6a1baab
Add new geolocation rules for French Guiana
kimandrews Jan 10, 2025
01c52d1
Add lat/longs for French Guiana
kimandrews Jan 10, 2025
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3 changes: 3 additions & 0 deletions ingest/defaults/geolocation_rules.tsv
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Expand Up @@ -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)/*/*
1 change: 1 addition & 0 deletions phylogenetic/defaults/config.yaml
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Expand Up @@ -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"
filter:
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1 change: 1 addition & 0 deletions phylogenetic/defaults/lat_longs.tsv
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@@ -0,0 +1 @@
country French Guiana (France) 4.0039882 -52.999998
2 changes: 2 additions & 0 deletions phylogenetic/rules/export.smk
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Expand Up @@ -15,6 +15,7 @@ rule export:
aa_muts = "results/aa_muts.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:
Expand All @@ -33,6 +34,7 @@ rule export:
--metadata-id-columns {params.strain_id} \
--node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} {input.year} \
--colors {input.colors} \
--lat-longs {input.lat_longs} \
--auspice-config {input.auspice_config} \
--include-root-sequence-inline \
--output {output.auspice_json} \
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