Initial commit

skills/phylo_from_buscos/scripts/convert_fasconcat_to_partition.py

@@ -0,0 +1,63 @@
+#!/usr/bin/env python3
+"""
+Convert FASconCAT info file to IQ-TREE partition format
+
+Usage:
+    python convert_fasconcat_to_partition.py FcC_info.xls [output_file.txt]
+
+Author: Bruno de Medeiros (Field Museum)
+Based on tutorials by Paul Frandsen (BYU)
+"""
+
+import sys
+
+
+def convert_fcc_to_partition(fcc_file, output_file="partition_def.txt"):
+    """
+    Convert FASconCAT info file to IQ-TREE partition format
+
+    Args:
+        fcc_file: Path to FcC_info.xls file from FASconCAT
+        output_file: Path to output partition definition file
+    """
+
+    try:
+        with open(fcc_file, 'r') as f:
+            lines = f.readlines()
+    except FileNotFoundError:
+        print(f"Error: File '{fcc_file}' not found")
+        sys.exit(1)
+
+    partitions_written = 0
+
+    with open(output_file, 'w') as out:
+        # Skip first two header lines (FASconCAT INFO and column headers)
+        for line in lines[2:]:
+            line = line.strip()
+            if line:
+                parts = line.split('\t')
+                if len(parts) >= 3:
+                    locus = parts[0]
+                    start = parts[1]
+                    end = parts[2]
+                    out.write(f"AA, {locus} = {start}-{end}\n")
+                    partitions_written += 1
+
+    print(f"Partition file created: {output_file}")
+    print(f"Number of partitions: {partitions_written}")
+
+
+def main():
+    if len(sys.argv) < 2:
+        print("Usage: python convert_fasconcat_to_partition.py FcC_info.xls [output_file.txt]")
+        print("\nConverts FASconCAT info file to IQ-TREE partition format")
+        sys.exit(1)
+
+    fcc_file = sys.argv[1]
+    output_file = sys.argv[2] if len(sys.argv) > 2 else "partition_def.txt"
+
+    convert_fcc_to_partition(fcc_file, output_file)
+
+
+if __name__ == "__main__":
+    main()