init python bindings

Author: nleroy917

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "genimtools"
-version = "0.0.2"
+version = "0.0.3"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

bindings/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "genimtools-py"
-version = "0.1.0"
+version = "0.0.3"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

bindings/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["maturin>=1.3,<2.0"]
 build-backend = "maturin"
 
 [project]
-name = "bindings"
+name = "genimtools"
 requires-python = ">=3.8"
 classifiers = [
     "Programming Language :: Rust",

bindings/src/functions.rs

@@ -0,0 +1,30 @@
+use std::io::Write;
+use std::fs::File;
+
+use pyo3::prelude::*;
+
+use genimtools::vocab::create_count_map;
+
+#[pyfunction]
+pub fn prune_universe(universe: &str, data: &str, min_count: Option<u32>, output: Option<&str>) -> PyResult<()> {
+    
+    let min_count = min_count.unwrap_or(1);
+    let output = output.unwrap_or("output.bed");
+
+    let cnt_map = create_count_map(data, universe).unwrap();
+
+    // create output file
+    let mut file = File::create(output).unwrap();
+    for (region, cnt) in cnt_map {
+        if cnt < min_count {
+            // skip this region
+            continue;
+        }
+        let line = format!("{}\t{}\t{}\n", region.chr, region.start, region.end);
+
+        // write to file
+        file.write_all(line.as_bytes())?;
+    }
+
+    Ok(())
+}

bindings/src/lib.rs

@@ -1,14 +1,11 @@
 use pyo3::prelude::*;
 
-/// Formats the sum of two numbers as string.
-#[pyfunction]
-fn sum_as_string(a: usize, b: usize) -> PyResult<String> {
-    Ok((a + b).to_string())
-}
+use crate::functions::prune_universe;
+
+mod functions;
 
-/// A Python module implemented in Rust.
 #[pymodule]
 fn genimtools(_py: Python, m: &PyModule) -> PyResult<()> {
-    m.add_function(wrap_pyfunction!(sum_as_string, m)?)?;
+    m.add_function(wrap_pyfunction!(prune_universe, m)?)?;
     Ok(())
-}
+}

docs/changelog.md

@@ -4,6 +4,9 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.0.3]
+- work on python bindings initialization
+
 ## [0.0.2]
 - prepare for first release