gtdb-tree

gtdb_tree

A library for parsing Newick format files, especially GTDB tree files.

Features

• Parse Newick formatted strings into a structured representation of trees.
• Handle various formats of Newick strings, including those with bootstrap values and distances.

Installation

Add this crate to your Cargo.toml:

[dependencies]
gtdb_tree = "0.1.9"

Usage

Here's a simple example of how to use the library:

use gtdb_tree::tree::parse_tree;

fn main() {
    let newick_str = "((A:0.1,B:0.2):0.3,C:0.4);";
    match parse_tree(newick_str) {
        Ok(nodes) => println!("Parsed nodes: {:?}", nodes),
        Err(e) => println!("Error parsing: {:?}", e),
    }
}

Python Usage

A Python package for parsing GTDB trees using Rust.

Installation

pip install gtdb_tree

import gtdb_tree

result = gtdb_tree.parse_tree("((A:0.1,B:0.2):0.3,C:0.4);")
print(result)

Advanced Usage

Custom Node Parser

You can provide a custom parser function to handle special node formats:

import gtdb_tree

def custom_parser(node_str):
    # Custom parsing logic
    name, length = node_str.split(':')
    return name, 100.0, float(length)  # name, bootstrap, length

result = gtdb_tree.parse_tree("((A:0.1,B:0.2):0.3,C:0.4);", custom_parser=custom_parser)
print(result)

Working with Node Objects

Each Node object in the result has the following attributes:

• id: Unique identifier for the node
• name: Name of the node
• bootstrap: Bootstrap value (if available)
• length: Branch length
• parent: ID of the parent node