Add Source-Target Gene Analysis Web Interface

src/indra_cogex/analysis/cli.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+import argparse
+import logging
+from datetime import datetime
+
+from indra_cogex.analysis.source_targets_explanation import explain_downstream
+
+logger = logging.getLogger(__name__)
+
+
+def main():
+    """Command line interface for running source-target analysis."""
+    parser = argparse.ArgumentParser(
+        description='Analyze mechanisms connecting source and target proteins using INDRA CoGEx.'
+    )
+    parser.add_argument('source',
+                        help='Source gene symbol or HGNC ID')
+    parser.add_argument('targets',
+                        nargs='+',
+                        help='Target gene symbols or HGNC IDs')
+    parser.add_argument(
+        '--id-type',
+        choices=['hgnc.symbol', 'hgnc'],
+        default='hgnc.symbol',
+        help='Type of identifiers provided (default: hgnc.symbol)'
+    )
+    parser.add_argument(
+        '--output-dir',
+        default=None,
+        help='Directory to save results (default: creates timestamped directory)'
+    )
+    parser.add_argument(
+        '--log-level',
+        default='INFO',
+        choices=['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'],
+        help='Set the logging level (default: INFO)'
+    )
+
+    args = parser.parse_args()
+
+    # Configure logging
+    logging.basicConfig(
+        level=getattr(logging, args.log_level),
+        format='%(asctime)s - %(name)s - %(levelname)s - %(message)s'
+    )
+
+    # Create output directory if not specified
+    if args.output_dir is None:
+        timestamp = datetime.now().strftime('%Y%m%d_%H%M%S')
+        args.output_dir = f'analysis_results_{timestamp}'
+
+    try:
+        # Run the analysis using the existing explain_downstream function
+        explain_downstream(
+            args.source,
+            args.targets,
+            args.output_dir,
+            id_type=args.id_type
+        )
+        logger.info(f'Analysis results saved to {args.output_dir}')
+
+    except Exception as e:
+        logger.error(f'Analysis failed: {str(e)}')
+        raise
+
+
+if __name__ == '__main__':
+    main()