From d8faead5c848e62bdc51f5281cde358808dd135b Mon Sep 17 00:00:00 2001
From: james hadfield <hadfield.james@gmail.com>
Date: Mon, 27 May 2024 16:37:51 +1200
Subject: [PATCH] Add Clade-I build

---
 .../defaults/clade-i/auspice_config.json      | 70 +++++++++++++++++++
 phylogenetic/defaults/clade-i/config.yaml     | 56 +++++++++++++++
 phylogenetic/defaults/clade-i/include.txt     |  0
 phylogenetic/rules/prepare_sequences.smk      |  6 ++
 4 files changed, 132 insertions(+)
 create mode 100644 phylogenetic/defaults/clade-i/auspice_config.json
 create mode 100644 phylogenetic/defaults/clade-i/config.yaml
 create mode 100644 phylogenetic/defaults/clade-i/include.txt

diff --git a/phylogenetic/defaults/clade-i/auspice_config.json b/phylogenetic/defaults/clade-i/auspice_config.json
new file mode 100644
index 00000000..a924efca
--- /dev/null
+++ b/phylogenetic/defaults/clade-i/auspice_config.json
@@ -0,0 +1,70 @@
+{
+  "title": "Genomic epidemiology of mpox clade I viruses",
+  "maintainers": [
+    {"name": "Nextstrain team", "url": "http://nextstrain.org"}
+  ],
+  "data_provenance": [
+    {
+      "name": "GenBank",
+      "url": "https://www.ncbi.nlm.nih.gov/genbank/"
+    }
+  ],
+  "build_url": "https://github.com/nextstrain/mpox",
+  "colorings": [
+    {
+      "key": "region",
+      "title": "Region",
+      "type": "categorical"
+    },
+    {
+      "key": "country",
+      "title": "Country",
+      "type": "categorical"
+    },
+    {
+      "key": "host",
+      "title": "Host",
+      "type": "categorical"
+    },
+    {
+      "key": "GA_CT_fraction",
+      "title": "G→A or C→T fraction",
+      "type": "continuous"
+    },
+    {
+      "key": "dinuc_context_fraction",
+      "title": "NGA/TCN context of G→A/C→T mutations",
+      "type": "continuous"
+    },
+    {
+      "key": "recency",
+      "title": "Submission Recency",
+      "type": "categorical"
+    },
+    {
+      "key": "date_submitted",
+      "title": "Release Date",
+      "type": "categorical"
+    },
+    {
+      "key": "date",
+      "title": "Collection date",
+      "type": "categorical"
+    }
+  ],
+  "geo_resolutions": [
+    "country"
+  ],
+  "display_defaults": {
+    "color_by": "country",
+    "map_triplicate": true,
+    "distance_measure": "num_date",
+    "transmission_lines": false
+  },
+  "filters": [
+    "country",
+    "region",
+    "recency",
+    "host"
+  ]
+}
diff --git a/phylogenetic/defaults/clade-i/config.yaml b/phylogenetic/defaults/clade-i/config.yaml
new file mode 100644
index 00000000..0f0d615b
--- /dev/null
+++ b/phylogenetic/defaults/clade-i/config.yaml
@@ -0,0 +1,56 @@
+reference: "defaults/reference.fasta"
+genome_annotation: "defaults/genome_annotation.gff3"
+genbank_reference: "defaults/reference.gb"
+include: "defaults/clade-i/include.txt"
+clades: "defaults/clades.tsv"
+lat_longs: "defaults/lat_longs.tsv"
+auspice_config: "defaults/clade-i/auspice_config.json"
+description: "defaults/description.md"
+tree_mask: "defaults/tree_mask.tsv"
+
+# Use `accession` as the ID column since `strain` currently contains duplicates¹.
+# ¹ https://github.com/nextstrain/mpox/issues/33
+strain_id_field: "accession"
+display_strain_field: "strain"
+
+build_name: "clade-i"
+auspice_name: "mpox_clade-I"
+
+filter:
+  min_date: 1900
+  min_length: 100000
+  exclude_where: 'clade!=I'
+
+
+### We don't want to subsample, so specify a config which is essentially a no-op
+subsample:
+  everything:
+    group_by: ""
+    sequences_per_group: ""
+
+## align
+max_indel: 10000
+seed_spacing: 1000
+
+## treefix
+fix_tree: true
+treefix_root: "" # without a root we'll midpoint root which should work great for clade I
+
+## refine
+timetree: true
+root: "best"
+clock_rate: 5.7e-5
+clock_std_dev: 2e-5
+divergence_units: "mutations"
+
+traits:
+  columns: "country"
+  sampling_bias_correction: 3
+
+## recency
+recency: true
+
+mask:
+  from_beginning: 800
+  from_end: 6422
+  maskfile: "defaults/mask.bed"
diff --git a/phylogenetic/defaults/clade-i/include.txt b/phylogenetic/defaults/clade-i/include.txt
new file mode 100644
index 00000000..e69de29b
diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
index c9ab5012..4916379a 100644
--- a/phylogenetic/rules/prepare_sequences.smk
+++ b/phylogenetic/rules/prepare_sequences.smk
@@ -65,6 +65,11 @@ rule filter:
         min_date=config["filter"]["min_date"],
         min_length=config["filter"]["min_length"],
         strain_id=config["strain_id_field"],
+        exclude_where=lambda w: (
+            f"--exclude-where {config['filter']['exclude_where']}"
+            if "exclude_where" in config["filter"]
+            else ""
+        ),
     shell:
         """
         augur filter \
@@ -74,6 +79,7 @@ rule filter:
             --output-sequences {output.sequences} \
             --output-metadata {output.metadata} \
             --exclude {input.exclude} \
+            {params.exclude_where} \
             --min-date {params.min_date} \
             --min-length {params.min_length} \
             --query "(QC_rare_mutations == 'good' | QC_rare_mutations == 'mediocre')" \