Initial commit

skills/clinical-reports/scripts/format_adverse_events.py

@@ -0,0 +1,103 @@
+#!/usr/bin/env python3
+"""
+Format adverse event data into tables for clinical trial reports.
+
+Converts CSV or structured data into formatted AE summary tables.
+
+Usage:
+    python format_adverse_events.py <ae_data.csv>
+"""
+
+import argparse
+import csv
+from collections import defaultdict
+from pathlib import Path
+
+
+def format_ae_summary_table(data: list) -> str:
+    """Generate AE summary table in markdown format."""
+    # Group by treatment arm
+    arm_stats = defaultdict(lambda: {
+        'total': 0,
+        'any_ae': 0,
+        'related_ae': 0,
+        'sae': 0,
+        'deaths': 0,
+        'discontinuations': 0
+    })
+    
+    for row in data:
+        arm = row.get('treatment_arm', 'Unknown')
+        arm_stats[arm]['total'] += 1
+        
+        if row.get('any_ae', '').lower() == 'yes':
+            arm_stats[arm]['any_ae'] += 1
+        if row.get('related', '').lower() == 'yes':
+            arm_stats[arm]['related_ae'] += 1
+        if row.get('serious', '').lower() == 'yes':
+            arm_stats[arm]['sae'] += 1
+        if row.get('fatal', '').lower() == 'yes':
+            arm_stats[arm]['deaths'] += 1
+        if row.get('discontinuation', '').lower() == 'yes':
+            arm_stats[arm]['discontinuations'] += 1
+    
+    # Generate table
+    table = "| Category | " + " | ".join(arm_stats.keys()) + " |\n"
+    table += "|----------|" + "|".join(["--------"] * len(arm_stats)) + "|\n"
+    
+    categories = [
+        ('Total N', 'total'),
+        ('Any AE', 'any_ae'),
+        ('Treatment-related AE', 'related_ae'),
+        ('Serious AE', 'sae'),
+        ('Deaths', 'deaths'),
+        ('Discontinuation due to AE', 'discontinuations')
+    ]
+    
+    for cat_name, cat_key in categories:
+        row_data = [cat_name]
+        for arm_data in arm_stats.values():
+            count = arm_data[cat_key]
+            total = arm_data['total']
+            pct = (count / total * 100) if total > 0 and cat_key != 'total' else 0
+            value = f"{count}" if cat_key == 'total' else f"{count} ({pct:.1f}%)"
+            row_data.append(value)
+        table += "| " + " | ".join(row_data) + " |\n"
+    
+    return table
+
+
+def main():
+    """Main entry point."""
+    parser = argparse.ArgumentParser(description="Format AE data into tables")
+    parser.add_argument("input_file", help="Path to AE data CSV")
+    parser.add_argument("--output", "-o", help="Output markdown file")
+    
+    args = parser.parse_args()
+    
+    try:
+        with open(args.input_file, 'r') as f:
+            reader = csv.DictReader(f)
+            data = list(reader)
+        
+        table = format_ae_summary_table(data)
+        
+        if args.output:
+            with open(args.output, 'w') as f:
+                f.write(table)
+            print(f"✓ Table saved to: {args.output}")
+        else:
+            print("\nAdverse Events Summary Table:\n")
+            print(table)
+        
+        return 0
+        
+    except Exception as e:
+        print(f"Error: {e}")
+        return 1
+
+
+if __name__ == "__main__":
+    import sys
+    sys.exit(main())
+