Add script to auto-extract reference sequences

mpxv-lineages · Aug 16, 2022 · 00c6c51 · 00c6c51
1 parent 958bb44
commit 00c6c51
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diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,4 @@
 package-lock.json
 .vscode/*
+auto-generated/reference_sequences.fasta
+auto-generated/reference_accessions.txt
diff --git a/scripts/generate-alias-key-json.py b/scripts/generate-alias-key-json.py
diff --git a/scripts/generate-single-file-json.py b/scripts/generate-single-file-json.py
diff --git a/scripts/get-reference-seqs.sh b/scripts/get-reference-seqs.sh
@@ -0,0 +1,26 @@
+#! bash
+
+# Remove file in case it exists
+rm auto-generated/reference_accessions.txt
+
+# Extract reference sequence accessions
+for file in lineages/*.yml; do
+    yq '.reference_sequences | .[].accession' $file >>auto-generated/reference_accessions.txt
+done
+
+# Error if there are duplicates
+
+if [ -n "$(sort auto-generated/reference_accessions.txt | uniq -cd)" ]; then
+    echo "Duplicate accessions found"
+    sort auto-generated/reference_accessions.txt | uniq -cd
+fi
+
+# Download and extract reference sequences
+curl -fsSL \
+    --compressed https://data.nextstrain.org/files/workflows/monkeypox/sequences.fasta.xz |
+    xz -d |
+    seqkit grep \
+        -f auto-generated/reference_accessions.txt \
+        -w0 \
+        --quiet \
+        >auto-generated/reference_sequences.fasta
diff --git a/scripts/validate-file-and-lineage-name.sh b/scripts/validate-file-and-lineage-name.sh
diff --git a/scripts/validate-lineage-yaml.sh b/scripts/validate-lineage-yaml.sh