Initial commit
This commit is contained in:
Zhongwei Li
229
skills/etetoolkit/scripts/tree_operations.py
Executable file
229
skills/etetoolkit/scripts/tree_operations.py
Executable file
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#!/usr/bin/env python3
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"""
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Tree operations helper script for common ETE toolkit tasks.
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Provides command-line interface for basic tree operations like:
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- Format conversion
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- Rooting (outgroup, midpoint)
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- Pruning
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- Basic statistics
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- ASCII visualization
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"""
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import argparse
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import sys
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from pathlib import Path
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try:
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from ete3 import Tree
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except ImportError:
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print("Error: ete3 not installed. Install with: pip install ete3")
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sys.exit(1)
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def load_tree(tree_file, format_num=0):
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"""Load tree from file."""
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try:
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return Tree(str(tree_file), format=format_num)
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except Exception as e:
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print(f"Error loading tree: {e}")
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sys.exit(1)
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def convert_format(tree_file, output, in_format=0, out_format=1):
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"""Convert tree between Newick formats."""
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tree = load_tree(tree_file, in_format)
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tree.write(outfile=str(output), format=out_format)
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print(f"Converted {tree_file} (format {in_format}) → {output} (format {out_format})")
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def reroot_tree(tree_file, output, outgroup=None, midpoint=False, format_num=0):
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"""Reroot tree by outgroup or midpoint."""
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tree = load_tree(tree_file, format_num)
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if midpoint:
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midpoint_node = tree.get_midpoint_outgroup()
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tree.set_outgroup(midpoint_node)
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print(f"Rerooted tree using midpoint method")
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elif outgroup:
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try:
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outgroup_node = tree & outgroup
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tree.set_outgroup(outgroup_node)
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print(f"Rerooted tree using outgroup: {outgroup}")
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except Exception as e:
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print(f"Error: Could not find outgroup '{outgroup}': {e}")
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sys.exit(1)
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else:
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print("Error: Must specify either --outgroup or --midpoint")
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sys.exit(1)
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tree.write(outfile=str(output), format=format_num)
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print(f"Saved rerooted tree to: {output}")
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def prune_tree(tree_file, output, keep_taxa, preserve_length=True, format_num=0):
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"""Prune tree to keep only specified taxa."""
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tree = load_tree(tree_file, format_num)
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# Read taxa list
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taxa_file = Path(keep_taxa)
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if taxa_file.exists():
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with open(taxa_file) as f:
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taxa = [line.strip() for line in f if line.strip()]
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else:
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taxa = [t.strip() for t in keep_taxa.split(",")]
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print(f"Pruning tree to {len(taxa)} taxa")
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try:
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tree.prune(taxa, preserve_branch_length=preserve_length)
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tree.write(outfile=str(output), format=format_num)
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print(f"Pruned tree saved to: {output}")
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print(f"Retained {len(tree)} leaves")
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except Exception as e:
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print(f"Error pruning tree: {e}")
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sys.exit(1)
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def tree_stats(tree_file, format_num=0):
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"""Display tree statistics."""
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tree = load_tree(tree_file, format_num)
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print(f"\n=== Tree Statistics ===")
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print(f"File: {tree_file}")
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print(f"Number of leaves: {len(tree)}")
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print(f"Total nodes: {len(list(tree.traverse()))}")
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farthest_leaf, distance = tree.get_farthest_leaf()
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print(f"Tree depth: {distance:.4f}")
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print(f"Farthest leaf: {farthest_leaf.name}")
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# Branch length statistics
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branch_lengths = [node.dist for node in tree.traverse() if not node.is_root()]
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if branch_lengths:
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print(f"\nBranch length statistics:")
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print(f" Mean: {sum(branch_lengths)/len(branch_lengths):.4f}")
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print(f" Min: {min(branch_lengths):.4f}")
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print(f" Max: {max(branch_lengths):.4f}")
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# Support values
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supports = [node.support for node in tree.traverse() if not node.is_leaf() and hasattr(node, 'support')]
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if supports:
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print(f"\nSupport value statistics:")
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print(f" Mean: {sum(supports)/len(supports):.2f}")
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print(f" Min: {min(supports):.2f}")
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print(f" Max: {max(supports):.2f}")
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print()
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def show_ascii(tree_file, format_num=0, show_internal=True):
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"""Display tree as ASCII art."""
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tree = load_tree(tree_file, format_num)
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print(tree.get_ascii(show_internal=show_internal))
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def list_leaves(tree_file, format_num=0):
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"""List all leaf names."""
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tree = load_tree(tree_file, format_num)
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for leaf in tree:
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print(leaf.name)
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def main():
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parser = argparse.ArgumentParser(
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description="ETE toolkit tree operations helper",
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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# Convert format
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%(prog)s convert input.nw output.nw --in-format 0 --out-format 1
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# Midpoint root
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%(prog)s reroot input.nw output.nw --midpoint
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# Reroot with outgroup
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%(prog)s reroot input.nw output.nw --outgroup "Outgroup_species"
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# Prune tree
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%(prog)s prune input.nw output.nw --keep-taxa "speciesA,speciesB,speciesC"
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# Show statistics
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%(prog)s stats input.nw
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# Display as ASCII
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%(prog)s ascii input.nw
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# List all leaves
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%(prog)s leaves input.nw
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"""
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)
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subparsers = parser.add_subparsers(dest="command", help="Command to execute")
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# Convert command
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convert_parser = subparsers.add_parser("convert", help="Convert tree format")
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convert_parser.add_argument("input", help="Input tree file")
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convert_parser.add_argument("output", help="Output tree file")
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convert_parser.add_argument("--in-format", type=int, default=0, help="Input format (default: 0)")
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convert_parser.add_argument("--out-format", type=int, default=1, help="Output format (default: 1)")
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# Reroot command
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reroot_parser = subparsers.add_parser("reroot", help="Reroot tree")
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reroot_parser.add_argument("input", help="Input tree file")
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reroot_parser.add_argument("output", help="Output tree file")
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reroot_parser.add_argument("--outgroup", help="Outgroup taxon name")
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reroot_parser.add_argument("--midpoint", action="store_true", help="Use midpoint rooting")
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reroot_parser.add_argument("--format", type=int, default=0, help="Newick format (default: 0)")
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# Prune command
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prune_parser = subparsers.add_parser("prune", help="Prune tree to specified taxa")
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prune_parser.add_argument("input", help="Input tree file")
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prune_parser.add_argument("output", help="Output tree file")
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prune_parser.add_argument("--keep-taxa", required=True,
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help="Taxa to keep (comma-separated or file path)")
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prune_parser.add_argument("--no-preserve-length", action="store_true",
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help="Don't preserve branch lengths")
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prune_parser.add_argument("--format", type=int, default=0, help="Newick format (default: 0)")
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# Stats command
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stats_parser = subparsers.add_parser("stats", help="Display tree statistics")
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stats_parser.add_argument("input", help="Input tree file")
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stats_parser.add_argument("--format", type=int, default=0, help="Newick format (default: 0)")
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# ASCII command
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ascii_parser = subparsers.add_parser("ascii", help="Display tree as ASCII art")
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ascii_parser.add_argument("input", help="Input tree file")
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ascii_parser.add_argument("--format", type=int, default=0, help="Newick format (default: 0)")
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ascii_parser.add_argument("--no-internal", action="store_true",
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help="Don't show internal node names")
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# Leaves command
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leaves_parser = subparsers.add_parser("leaves", help="List all leaf names")
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leaves_parser.add_argument("input", help="Input tree file")
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leaves_parser.add_argument("--format", type=int, default=0, help="Newick format (default: 0)")
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args = parser.parse_args()
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if not args.command:
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parser.print_help()
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sys.exit(1)
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# Execute command
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if args.command == "convert":
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convert_format(args.input, args.output, args.in_format, args.out_format)
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elif args.command == "reroot":
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reroot_tree(args.input, args.output, args.outgroup, args.midpoint, args.format)
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elif args.command == "prune":
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prune_tree(args.input, args.output, args.keep_taxa,
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not args.no_preserve_length, args.format)
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elif args.command == "stats":
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tree_stats(args.input, args.format)
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elif args.command == "ascii":
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show_ascii(args.input, args.format, not args.no_internal)
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elif args.command == "leaves":
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list_leaves(args.input, args.format)
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if __name__ == "__main__":
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main()
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