Initial commit

scientific-packages/arboreto/scripts/basic_grn_inference.py

@@ -0,0 +1,110 @@
+#!/usr/bin/env python3
+"""
+Basic GRN inference script using arboreto GRNBoost2.
+
+This script demonstrates the standard workflow for gene regulatory network inference:
+1. Load expression data
+2. Optionally load transcription factor names
+3. Run GRNBoost2 inference
+4. Save results
+
+Usage:
+    python basic_grn_inference.py <expression_file> [options]
+
+Example:
+    python basic_grn_inference.py expression_data.tsv -t tf_names.txt -o network.tsv
+"""
+
+import argparse
+import pandas as pd
+from arboreto.algo import grnboost2
+from arboreto.utils import load_tf_names
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='Infer gene regulatory network using GRNBoost2'
+    )
+    parser.add_argument(
+        'expression_file',
+        help='Path to expression data file (TSV/CSV format)'
+    )
+    parser.add_argument(
+        '-t', '--tf-file',
+        help='Path to file containing transcription factor names (one per line)',
+        default=None
+    )
+    parser.add_argument(
+        '-o', '--output',
+        help='Output file path for network results',
+        default='network_output.tsv'
+    )
+    parser.add_argument(
+        '-s', '--seed',
+        type=int,
+        help='Random seed for reproducibility',
+        default=42
+    )
+    parser.add_argument(
+        '--sep',
+        help='Separator for input file (default: tab)',
+        default='\t'
+    )
+    parser.add_argument(
+        '--transpose',
+        action='store_true',
+        help='Transpose the expression matrix (use if genes are rows)'
+    )
+
+    args = parser.parse_args()
+
+    # Load expression data
+    print(f"Loading expression data from {args.expression_file}...")
+    expression_data = pd.read_csv(args.expression_file, sep=args.sep, index_col=0)
+
+    # Transpose if needed
+    if args.transpose:
+        print("Transposing expression matrix...")
+        expression_data = expression_data.T
+
+    print(f"Expression data shape: {expression_data.shape}")
+    print(f"  Observations (rows): {expression_data.shape[0]}")
+    print(f"  Genes (columns): {expression_data.shape[1]}")
+
+    # Load TF names if provided
+    tf_names = None
+    if args.tf_file:
+        print(f"Loading transcription factor names from {args.tf_file}...")
+        tf_names = load_tf_names(args.tf_file)
+        print(f"  Found {len(tf_names)} transcription factors")
+    else:
+        print("No TF file provided. Using all genes as potential regulators.")
+
+    # Run GRNBoost2
+    print("\nRunning GRNBoost2 inference...")
+    print("  (This may take a while depending on dataset size)")
+
+    network = grnboost2(
+        expression_data=expression_data,
+        tf_names=tf_names,
+        seed=args.seed
+    )
+
+    print(f"\nInference complete!")
+    print(f"  Total regulatory links inferred: {len(network)}")
+    print(f"  Unique TFs: {network['TF'].nunique()}")
+    print(f"  Unique targets: {network['target'].nunique()}")
+
+    # Save results
+    print(f"\nSaving results to {args.output}...")
+    network.to_csv(args.output, sep='\t', index=False)
+
+    # Display top 10 predictions
+    print("\nTop 10 predicted regulatory relationships:")
+    print(network.head(10).to_string(index=False))
+
+    print("\nDone!")
+
+
+if __name__ == '__main__':
+    main()