20251125

99.scripts/workflow/phylogeny_reconstruction/06.alignments_to_nexus.sh

@@ -0,0 +1,18 @@
+#! /usr/bin/env bash
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <input_fasta_dir> <extension> <output_nexus_dir>"
+    exit 1
+fi
+
+input_dir=$1
+extension=$2
+output_dir=$3
+mkdir -p "${output_dir}"
+for f in "${input_dir}"/*."${extension}"; do
+    filename=$(basename -- "${f}")
+    filename_noext="${filename%.*}"
+    output_file="${output_dir}/${filename_noext}.nex"
+    echo "Converting ${f} to ${output_file}"
+    seqmagick convert --output-format nexus --alphabet dna --input-format fasta "${f}" "${output_file}"
+done