Initial commit

skills/phylo_from_buscos/scripts/rename_genomes.py

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+#!/usr/bin/env python3
+"""
+Rename genome files with clean, meaningful sample names for phylogenomics
+
+This script helps create a mapping between genome files (often with cryptic
+accession numbers) and clean species/sample names that will appear in the
+final phylogenetic tree.
+
+Usage:
+    # Interactive mode - prompts for names
+    python rename_genomes.py --interactive genome1.fasta genome2.fasta
+
+    # From mapping file (TSV: old_name<TAB>new_name)
+    python rename_genomes.py --mapping samples.tsv
+
+    # Create template mapping file
+    python rename_genomes.py --create-template *.fasta > samples.tsv
+
+Author: Bruno de Medeiros (Field Museum)
+Based on tutorials by Paul Frandsen (BYU)
+"""
+
+import argparse
+import os
+import sys
+import shutil
+from pathlib import Path
+
+
+def sanitize_name(name):
+    """
+    Sanitize a name to be phylogenomics-safe
+    - Replace spaces with underscores
+    - Remove special characters
+    - Keep only alphanumeric, underscore, hyphen
+    """
+    # Replace spaces with underscores
+    name = name.replace(' ', '_')
+    # Remove special characters except underscore and hyphen
+    name = ''.join(c for c in name if c.isalnum() or c in '_-')
+    return name
+
+
+def create_template(genome_files, output=sys.stdout):
+    """Create a template mapping file"""
+    output.write("# Sample mapping file\n")
+    output.write("# Format: original_filename<TAB>new_sample_name\n")
+    output.write("# Edit the second column with meaningful species/sample names\n")
+    output.write("# Recommended format: [ACCESSION]_[NAME] (e.g., GCA000123456_Penstemon_eatonii)\n")
+    output.write("# This keeps accession for traceability while having readable names in trees\n")
+    output.write("# Names should contain only letters, numbers, underscores, and hyphens\n")
+    output.write("#\n")
+
+    for gfile in genome_files:
+        basename = Path(gfile).stem  # Remove extension
+        output.write(f"{gfile}\t{basename}\n")
+
+
+def read_mapping(mapping_file):
+    """Read mapping from TSV file"""
+    mapping = {}
+    with open(mapping_file, 'r') as f:
+        for line in f:
+            line = line.strip()
+            # Skip comments and empty lines
+            if not line or line.startswith('#'):
+                continue
+
+            parts = line.split('\t')
+            if len(parts) != 2:
+                print(f"Warning: Skipping invalid line: {line}", file=sys.stderr)
+                continue
+
+            old_name, new_name = parts
+            new_name = sanitize_name(new_name)
+            mapping[old_name] = new_name
+
+    return mapping
+
+
+def interactive_rename(genome_files):
+    """Interactively ask for new names"""
+    mapping = {}
+
+    print("Enter new sample names for each genome file.")
+    print("Press Enter to keep the current name.")
+    print("Names will be sanitized (spaces→underscores, special chars removed)\n")
+
+    for gfile in genome_files:
+        current_name = Path(gfile).stem
+        new_name = input(f"{gfile} → [{current_name}]: ").strip()
+
+        if not new_name:
+            new_name = current_name
+
+        new_name = sanitize_name(new_name)
+        mapping[gfile] = new_name
+        print(f"  Will rename to: {new_name}.fasta\n")
+
+    return mapping
+
+
+def rename_files(mapping, dry_run=False, backup=True):
+    """Rename genome files according to mapping"""
+
+    renamed = []
+    errors = []
+
+    for old_file, new_name in mapping.items():
+        if not os.path.exists(old_file):
+            errors.append(f"File not found: {old_file}")
+            continue
+
+        # Get extension from original file
+        ext = Path(old_file).suffix
+        if not ext:
+            ext = '.fasta'
+
+        new_file = f"{new_name}{ext}"
+
+        # Check if target exists
+        if os.path.exists(new_file) and new_file != old_file:
+            errors.append(f"Target exists: {new_file}")
+            continue
+
+        # Skip if names are the same
+        if old_file == new_file:
+            print(f"Skip (no change): {old_file}")
+            continue
+
+        if dry_run:
+            print(f"[DRY RUN] Would rename: {old_file} → {new_file}")
+        else:
+            # Backup if requested
+            if backup:
+                backup_file = f"{old_file}.backup"
+                shutil.copy2(old_file, backup_file)
+                print(f"Backup created: {backup_file}")
+
+            # Rename
+            shutil.move(old_file, new_file)
+            print(f"Renamed: {old_file} → {new_file}")
+            renamed.append((old_file, new_file))
+
+    return renamed, errors
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Rename genome files with meaningful sample names for phylogenomics",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  # Create template mapping file
+  python rename_genomes.py --create-template *.fasta > samples.tsv
+  # Edit samples.tsv, then apply mapping
+  python rename_genomes.py --mapping samples.tsv
+
+  # Interactive renaming
+  python rename_genomes.py --interactive genome1.fasta genome2.fasta
+
+  # Dry run (preview changes)
+  python rename_genomes.py --mapping samples.tsv --dry-run
+        """
+    )
+
+    group = parser.add_mutually_exclusive_group(required=True)
+    group.add_argument(
+        '--create-template',
+        nargs='+',
+        metavar='GENOME',
+        help='Create a template mapping file from genome files'
+    )
+    group.add_argument(
+        '--mapping',
+        metavar='FILE',
+        help='TSV file with mapping (old_name<TAB>new_name)'
+    )
+    group.add_argument(
+        '--interactive',
+        nargs='+',
+        metavar='GENOME',
+        help='Interactively rename genome files'
+    )
+
+    parser.add_argument(
+        '--dry-run',
+        action='store_true',
+        help='Show what would be renamed without actually renaming'
+    )
+
+    parser.add_argument(
+        '--no-backup',
+        action='store_true',
+        help='Do not create backup files'
+    )
+
+    args = parser.parse_args()
+
+    # Create template
+    if args.create_template:
+        create_template(args.create_template)
+        return
+
+    # Interactive mode
+    if args.interactive:
+        mapping = interactive_rename(args.interactive)
+    # Mapping file mode
+    elif args.mapping:
+        mapping = read_mapping(args.mapping)
+    else:
+        parser.error("No mode specified")
+
+    if not mapping:
+        print("No files to rename", file=sys.stderr)
+        return
+
+    # Perform renaming
+    renamed, errors = rename_files(
+        mapping,
+        dry_run=args.dry_run,
+        backup=not args.no_backup
+    )
+
+    # Summary
+    print("\n" + "="*60)
+    if args.dry_run:
+        print("DRY RUN - No files were actually renamed")
+    else:
+        print(f"Successfully renamed {len(renamed)} file(s)")
+
+    if errors:
+        print(f"\nErrors ({len(errors)}):")
+        for error in errors:
+            print(f"  - {error}")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()