A library for parsing Newick format files, especially GTDB tree files.
- Parse Newick formatted strings into a structured representation of trees.
- Handle various formats of Newick strings, including those with bootstrap values and distances.
Add this crate to your Cargo.toml:
[dependencies] gtdb_tree = "0.1.9"
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), } }
A Python package for parsing GTDB trees using Rust.
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)
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)
- 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