Consolidate skills

scientific-skills/deeptools/scripts/validate_files.py

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+#!/usr/bin/env python3
+"""
+deepTools File Validation Script
+
+Validates BAM, bigWig, and BED files for deepTools analysis.
+Checks for file existence, proper indexing, and basic format requirements.
+"""
+
+import os
+import sys
+import argparse
+from pathlib import Path
+
+
+def check_file_exists(filepath):
+    """Check if file exists and is readable."""
+    if not os.path.exists(filepath):
+        return False, f"File not found: {filepath}"
+    if not os.access(filepath, os.R_OK):
+        return False, f"File not readable: {filepath}"
+    return True, f"✓ File exists: {filepath}"
+
+
+def check_bam_index(bam_file):
+    """Check if BAM file has an index (.bai or .bam.bai)."""
+    bai_file1 = bam_file + ".bai"
+    bai_file2 = bam_file.replace(".bam", ".bai")
+
+    if os.path.exists(bai_file1):
+        return True, f"✓ BAM index found: {bai_file1}"
+    elif os.path.exists(bai_file2):
+        return True, f"✓ BAM index found: {bai_file2}"
+    else:
+        return False, f"✗ BAM index missing for: {bam_file}\n  Run: samtools index {bam_file}"
+
+
+def check_bigwig_file(bw_file):
+    """Basic check for bigWig file."""
+    # Check file size (bigWig files should have reasonable size)
+    file_size = os.path.getsize(bw_file)
+    if file_size < 100:
+        return False, f"✗ bigWig file suspiciously small: {bw_file} ({file_size} bytes)"
+    return True, f"✓ bigWig file appears valid: {bw_file} ({file_size} bytes)"
+
+
+def check_bed_file(bed_file):
+    """Basic validation of BED file format."""
+    try:
+        with open(bed_file, 'r') as f:
+            lines = [line.strip() for line in f if line.strip() and not line.startswith('#')]
+
+        if len(lines) == 0:
+            return False, f"✗ BED file is empty: {bed_file}"
+
+        # Check first few lines for basic format
+        for i, line in enumerate(lines[:10], 1):
+            fields = line.split('\t')
+            if len(fields) < 3:
+                return False, f"✗ BED file format error at line {i}: expected at least 3 columns\n  Line: {line}"
+
+            # Check if start and end are integers
+            try:
+                start = int(fields[1])
+                end = int(fields[2])
+                if start >= end:
+                    return False, f"✗ BED file error at line {i}: start >= end ({start} >= {end})"
+            except ValueError:
+                return False, f"✗ BED file format error at line {i}: start and end must be integers\n  Line: {line}"
+
+        return True, f"✓ BED file format appears valid: {bed_file} ({len(lines)} regions)"
+
+    except Exception as e:
+        return False, f"✗ Error reading BED file: {bed_file}\n  Error: {str(e)}"
+
+
+def validate_files(bam_files=None, bigwig_files=None, bed_files=None):
+    """
+    Validate all provided files.
+
+    Args:
+        bam_files: List of BAM file paths
+        bigwig_files: List of bigWig file paths
+        bed_files: List of BED file paths
+
+    Returns:
+        Tuple of (success: bool, messages: list)
+    """
+    all_success = True
+    messages = []
+
+    # Validate BAM files
+    if bam_files:
+        messages.append("\n=== Validating BAM Files ===")
+        for bam_file in bam_files:
+            # Check existence
+            success, msg = check_file_exists(bam_file)
+            messages.append(msg)
+            if not success:
+                all_success = False
+                continue
+
+            # Check index
+            success, msg = check_bam_index(bam_file)
+            messages.append(msg)
+            if not success:
+                all_success = False
+
+    # Validate bigWig files
+    if bigwig_files:
+        messages.append("\n=== Validating bigWig Files ===")
+        for bw_file in bigwig_files:
+            # Check existence
+            success, msg = check_file_exists(bw_file)
+            messages.append(msg)
+            if not success:
+                all_success = False
+                continue
+
+            # Basic bigWig check
+            success, msg = check_bigwig_file(bw_file)
+            messages.append(msg)
+            if not success:
+                all_success = False
+
+    # Validate BED files
+    if bed_files:
+        messages.append("\n=== Validating BED Files ===")
+        for bed_file in bed_files:
+            # Check existence
+            success, msg = check_file_exists(bed_file)
+            messages.append(msg)
+            if not success:
+                all_success = False
+                continue
+
+            # Check BED format
+            success, msg = check_bed_file(bed_file)
+            messages.append(msg)
+            if not success:
+                all_success = False
+
+    return all_success, messages
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Validate files for deepTools analysis",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  # Validate BAM files
+  python validate_files.py --bam sample1.bam sample2.bam
+
+  # Validate all file types
+  python validate_files.py --bam input.bam chip.bam --bed peaks.bed --bigwig signal.bw
+
+  # Validate from a directory
+  python validate_files.py --bam *.bam --bed *.bed
+        """
+    )
+
+    parser.add_argument('--bam', nargs='+', help='BAM files to validate')
+    parser.add_argument('--bigwig', '--bw', nargs='+', help='bigWig files to validate')
+    parser.add_argument('--bed', nargs='+', help='BED files to validate')
+
+    args = parser.parse_args()
+
+    # Check if any files were provided
+    if not any([args.bam, args.bigwig, args.bed]):
+        parser.print_help()
+        sys.exit(1)
+
+    # Run validation
+    success, messages = validate_files(
+        bam_files=args.bam,
+        bigwig_files=args.bigwig,
+        bed_files=args.bed
+    )
+
+    # Print results
+    for msg in messages:
+        print(msg)
+
+    # Summary
+    print("\n" + "="*50)
+    if success:
+        print("✓ All validations passed!")
+        sys.exit(0)
+    else:
+        print("✗ Some validations failed. Please fix the issues above.")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()