custom parser

Author: dagou

Cargo.lock

@@ -1,6 +1,6 @@
 [package]
 name = "gtdb_tree"
-version = "0.1.8"
+version = "0.1.9"
 edition = "2021"
 description = "A library for parsing Newick format files, especially GTDB tree files."
 homepage = "https://github.com/eric9n/gtdb_tree"

Cargo.toml

@@ -13,7 +13,7 @@ Add this crate to your `Cargo.toml`:
 
 ```toml
 [dependencies]
-gtdb_tree = "0.1.0"
+gtdb_tree = "0.1.9"
 ```
 
 ## Usage
@@ -48,3 +48,27 @@ 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:
+
+```python
+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

README.md

@@ -9,7 +9,7 @@ features = ["python"]
 
 [project]
 name = "gtdb_tree"
-version = "0.1.8"
+version = "0.1.9"
 description = "A Python package for parsing GTDB trees using Rust"
 readme = "README.md"
 authors = [{ name = "dagou", email = "[email protected]" }]

pyproject.toml

@@ -3,7 +3,7 @@
 
 setup(
     name="gtdb_tree",
-    version="0.1.8",
+    version="0.1.9",
     rust_extensions=[RustExtension("gtdb_tree.gtdb_tree", binding=Binding.PyO3)],
     packages=["gtdb_tree"],
     # rust extensions are not zip safe, just like C-extensions.

setup.py

@@ -22,13 +22,15 @@ pub enum ParseError {
     UnexpectedEndOfInput,
     #[allow(dead_code)]
     InvalidFormat(String),
+    PythonError(String),
 }
 
 impl std::fmt::Display for ParseError {
     fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
         match self {
             ParseError::UnexpectedEndOfInput => write!(f, "Unexpected end of input"),
             ParseError::InvalidFormat(msg) => write!(f, "Invalid format: {}", msg),
+            ParseError::PythonError(msg) => write!(f, "Python error: {}", msg),
         }
     }
 }

src/node.rs

@@ -1,5 +1,15 @@
 use crate::node::Node as RustNode;
-use crate::tree;
+use crate::node::ParseError;
+use crate::tree::{self, NodeParser};
+use std::convert::From;
+use std::sync::Arc;
+
+// 添加一个从 PyErr 到 ParseError 的转换实现
+impl From<PyErr> for ParseError {
+    fn from(err: PyErr) -> Self {
+        ParseError::PythonError(err.to_string())
+    }
+}
 
 #[cfg(feature = "python")]
 use pyo3::prelude::*;
@@ -39,10 +49,94 @@ impl Node {
     }
 }
 
+// #[cfg(feature = "python")]
+// #[pyfunction]
+// pub fn parse_tree(newick_str: &str) -> PyResult<Vec<Node>> {
+//     tree::parse_tree(newick_str)
+//         .map(|rust_nodes| rust_nodes.into_iter().map(|rn| Node { node: rn }).collect())
+//         .map_err(|e| PyErr::new::<pyo3::exceptions::PyValueError, _>(e.to_string()))
+// }
+
 #[cfg(feature = "python")]
 #[pyfunction]
-pub fn parse_tree(newick_str: &str) -> PyResult<Vec<Node>> {
-    tree::parse_tree(newick_str)
+#[pyo3(signature = (newick_str, custom_parser = None))]
+#[pyo3(text_signature = "(newick_str, custom_parser=None)")]
+/// Parse a Newick format string into a list of Node objects.
+///
+/// This function takes a Newick format string and optionally a custom parser function,
+/// and returns a list of Node objects representing the phylogenetic tree.
+///
+/// Parameters:
+/// -----------
+/// newick_str : str
+///     The Newick format string representing the phylogenetic tree.
+/// custom_parser : callable, optional
+///     A custom parsing function for node information. If not provided, the default parser will be used.
+///     The custom parser should have the following signature:
+///
+///     def custom_parser(node_str: str) -> Tuple[str, float, float]:
+///         '''
+///         Parse a node string and return name, bootstrap, and length.
+///
+///         Parameters:
+///         -----------
+///         node_str : str
+///             The node string to parse.
+///
+///         Returns:
+///         --------
+///         Tuple[str, float, float]
+///             A tuple containing (name, bootstrap, length) for the node.
+///         '''
+///         # Your custom parsing logic here
+///         return name, bootstrap, length
+///
+/// Returns:
+/// --------
+/// List[Node]
+///     A list of Node objects representing the parsed phylogenetic tree.
+///
+/// Raises:
+/// -------
+/// ValueError
+///     If the Newick string is invalid or parsing fails.
+///
+/// Example:
+/// --------
+/// >>> newick_str = "(A:0.1,B:0.2,(C:0.3,D:0.4)70:0.5);"
+/// >>> nodes = parse_tree(newick_str)
+/// >>>
+/// >>> # Using a custom parser
+/// >>> def my_parser(node_str):
+/// ...     parts = node_str.split(':')
+/// ...     name = parts[0]
+/// ...     length = float(parts[1]) if len(parts) > 1 else 0.0
+/// ...     return name, 100.0, length  # Always set bootstrap to 100.0
+/// >>>
+/// >>> nodes_custom = parse_tree(newick_str, custom_parser=my_parser)
+pub fn parse_tree(
+    _py: Python,
+    newick_str: &str,
+    custom_parser: Option<PyObject>,
+) -> PyResult<Vec<Node>> {
+    let parser = match custom_parser {
+        Some(py_func) => {
+            let py_func = Arc::new(py_func);
+            NodeParser::Custom(Box::new(
+                move |node_str: &str| -> Result<(String, f64, f64), ParseError> {
+                    Python::with_gil(|py| {
+                        let result = py_func.call1(py, (node_str,))?;
+                        let (name, bootstrap, length): (String, f64, f64) = result.extract(py)?;
+                        Ok((name, bootstrap, length))
+                    })
+                    .map_err(|e: PyErr| ParseError::PythonError(e.to_string()))
+                },
+            ))
+        }
+        None => NodeParser::Default,
+    };
+
+    tree::parse_tree(newick_str, parser)
         .map(|rust_nodes| rust_nodes.into_iter().map(|rn| Node { node: rn }).collect())
         .map_err(|e| PyErr::new::<pyo3::exceptions::PyValueError, _>(e.to_string()))
 }

src/python.rs

@@ -1,6 +1,26 @@
 use crate::node::{Node, ParseError};
 use memchr::memchr2;
 
+// 修改 NodeParser 枚举以使用 trait 对象
+pub enum NodeParser {
+    Default,
+    Custom(Box<dyn Fn(&str) -> Result<(String, f64, f64), ParseError> + Send>),
+}
+
+impl Default for NodeParser {
+    fn default() -> Self {
+        NodeParser::Default
+    }
+}
+
+/// Parse the label of a node from a Newick tree string.
+///
+/// This function takes a byte slice representing a node in a Newick tree string,
+/// and returns the name and length of the node as a tuple.
+///
+/// # Arguments
+///
+/// * `label` - A string slice representing the node in a Newick tree string.
 fn parse_label(label: &str) -> Result<(String, f64), ParseError> {
     let label = label.trim_end_matches(";").trim_matches('\'').to_string();
 
@@ -31,27 +51,41 @@ fn parse_label(label: &str) -> Result<(String, f64), ParseError> {
 ///
 /// # Arguments
 ///
-/// * `node_bytes` - A byte slice representing the node in a Newick tree string.
+/// * `node_str` - A string slice representing the node in a Newick tree string.
 ///
 /// # Returns
 ///
-/// Returns a `Result` containing a tuple of the name and length on success,
+/// Returns a `Result` containing a tuple of the name, bootstrap, and length on success,
 /// or an `Err(ParseError)` on failure.
 ///
 /// # Example
 ///
 /// ```
-/// use gtdb_tree::tree::parse_node;
+/// use gtdb_tree::tree::parse_node_default;
 ///
-/// let node_bytes = b"A:0.1";
-/// let (name, bootstrap, length) = parse_node(node_bytes).unwrap();
+/// let node_str = "A:0.1";
+/// let (name, bootstrap, length) = parse_node_default(node_str).unwrap();
 /// assert_eq!(name, "A");
 /// assert_eq!(bootstrap, 0.0);
 /// assert_eq!(length, 0.1);
 /// ```
-pub fn parse_node(node_bytes: &[u8]) -> Result<(String, f64, f64), ParseError> {
-    let node_str = std::str::from_utf8(node_bytes).expect("UTF-8 sequence");
-    // gtdb
+pub fn parse_node_default(node_str: &str) -> Result<(String, f64, f64), ParseError> {
+    // 处理 "AD:0.03347[21.0]" 格式
+    if let Some((name_length, bootstrap_str)) = node_str.rsplit_once('[') {
+        if let Some((name, length_str)) = name_length.rsplit_once(':') {
+            let bootstrap = bootstrap_str
+                .trim_end_matches(']')
+                .parse::<f64>()
+                .map_err(|_| {
+                    ParseError::InvalidFormat(format!("Invalid bootstrap value: {}", bootstrap_str))
+                })?;
+            let length = length_str.parse::<f64>().map_err(|_| {
+                ParseError::InvalidFormat(format!("Invalid length value: {}", length_str))
+            })?;
+            return Ok((name.to_string(), bootstrap, length));
+        }
+    }
+
     // Check if node_str contains single quotes and ensure they are together
     if node_str.matches('\'').count() % 2 != 0 {
         return Err(ParseError::InvalidFormat(format!(
@@ -102,12 +136,13 @@ pub fn parse_node(node_bytes: &[u8]) -> Result<(String, f64, f64), ParseError> {
 ///
 /// ```
 /// use gtdb_tree::tree::parse_tree;
+/// use gtdb_tree::tree::NodeParser;
 ///
 /// let newick_str = "((A:0.1,B:0.2):0.3,C:0.4);";
-/// let nodes = parse_tree(newick_str).unwrap();
+/// let nodes = parse_tree(newick_str, NodeParser::default()).unwrap();
 /// assert_eq!(nodes.len(), 5);
 /// ```
-pub fn parse_tree(newick_str: &str) -> Result<Vec<Node>, ParseError> {
+pub fn parse_tree(newick_str: &str, parser: NodeParser) -> Result<Vec<Node>, ParseError> {
     let mut nodes: Vec<Node> = Vec::new();
     let mut pos = 0;
 
@@ -132,7 +167,16 @@ pub fn parse_tree(newick_str: &str) -> Result<Vec<Node>, ParseError> {
                 let end_pos = memchr2(b',', b')', &bytes[pos..]).unwrap_or(bytes_len - pos);
                 let node_end_pos = pos + end_pos;
                 let node_bytes = &bytes[pos..node_end_pos];
-                let (name, bootstrap, length) = parse_node(node_bytes)?;
+
+                let mut node_str = std::str::from_utf8(node_bytes).expect("UTF-8 sequence");
+                if node_end_pos == bytes_len {
+                    node_str = node_str.trim_end_matches(';');
+                }
+                let (name, bootstrap, length) = match &parser {
+                    NodeParser::Default => parse_node_default(node_str)?,
+                    NodeParser::Custom(func) => func(node_str)?,
+                };
+
                 let node_id = if &bytes[pos - 1] == &b')' {
                     stack.pop().unwrap_or(0)
                 } else {
@@ -161,8 +205,9 @@ mod tests {
     use super::*;
 
     #[test]
-    fn test_parse_tree() {
+    fn test_parse_tree() -> Result<(), ParseError> {
         let test_cases = vec![
+            "(A:0.1,B:0.2,(C:0.3,D:0.4)AD:0.03347[21.0]);",
             "((A:0.1,B:0.2)'56:F;H;':0.3,C:0.4);",
             "(,,(,));",                            // no nodes are named
             "(A,B,(C,D));",                        // leaf nodes are named
@@ -175,15 +220,15 @@ mod tests {
         ];
 
         for newick_str in test_cases {
-            match parse_tree(newick_str) {
-                Ok(nodes) => println!(
-                    "Parsed nodes for '{}': {:?}, len: {}",
-                    newick_str,
-                    nodes,
-                    nodes.len()
-                ),
-                Err(e) => println!("Error parsing '{}': {:?}", newick_str, e),
-            }
+            let nodes = parse_tree(newick_str, NodeParser::default())?;
+            println!(
+                "Parsed nodes for '{}': {:?}, len: {}",
+                newick_str,
+                nodes,
+                nodes.len()
+            )
         }
+
+        Ok(())
     }
 }