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Cargo.toml

@@ -0,0 +1,15 @@
+[package]
+name = "pandora_lib_bindings"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+anyhow = "^1.0.75"
+uuid = { version = "1.6.1", features = ["serde", "v4"] }
+log = "^0.4.20"
+env_logger = "^0.10.1"
+indicatif = "0.17.8"
+tokio = { version = "1", features = ["full"] }
+futures = "0.3.30"
+regex = "1.10.4"
+

src/lib.rs

@@ -0,0 +1,30 @@
+pub mod progs;
+pub mod utils;
+
+#[cfg(test)]
+mod tests {
+    use env_logger::Env;
+    use crate::utils::Run;
+
+    use self::progs::cramino::Cramino;
+
+    use super::*;
+    fn init() {
+        let _ = env_logger::Builder::from_env(Env::default().default_filter_or("info"))
+            .is_test(true)
+            .try_init();
+    }
+
+    #[test]
+    fn it_works() -> anyhow::Result<()> {
+        init();
+        let mut cramino = Cramino::default()
+            .with_threads(150)
+            .with_result_path("/data/longreads_basic_pipe/CAMARA/diag/CAMARA_diag_hs1_cramino.txt")
+            .with_bam("/data/longreads_basic_pipe/CAMARA/diag/CAMARA_diag_hs1.bam")?;
+        cramino.run()?;
+        println!("{cramino:?}");
+        assert!(cramino.results.unwrap().is_woman()?);
+        Ok(())
+    }
+}

src/progs/cramino.rs

@@ -0,0 +1,181 @@
+use std::{
+    collections::HashMap,
+    env,
+    fs::{self, File},
+    io::{self, BufRead},
+    path::PathBuf,
+};
+
+use anyhow::anyhow;
+use log::info;
+use uuid::Uuid;
+
+use crate::utils::{exec_bin_to_file, RunBin};
+
+#[derive(Debug)]
+pub struct Cramino {
+    pub prog_path: String,
+    pub args: Vec<String>,
+    pub bam_file: PathBuf,
+    pub result_path: PathBuf,
+    pub results: Option<CraminoRes>,
+    pub remove_result_file: bool,
+}
+
+impl Default for Cramino {
+    fn default() -> Self {
+        let mut result_path = env::temp_dir();
+        result_path.push(format!("{}_cramino.txt", Uuid::new_v4()));
+
+        Self {
+            prog_path: "cramino".to_string(),
+            args: vec![
+                "--hist".to_string(),
+                "--checksum".to_string(),
+                "--karyotype".to_string(),
+            ],
+            result_path,
+            results: None,
+            remove_result_file: false,
+            bam_file: PathBuf::new(),
+        }
+    }
+}
+
+impl Cramino {
+    pub fn with_result_path(mut self, result_path: &str) -> Self {
+        self.result_path = PathBuf::from(result_path);
+        self
+    }
+
+    pub fn with_threads(mut self, n_threads: usize) -> Self {
+        self.args.push("-t".to_string());
+        self.args.push(n_threads.to_string());
+        self
+    }
+
+    pub fn with_bam(mut self, bam_file: &str) -> anyhow::Result<Self> {
+        let bam_file = PathBuf::from(bam_file);
+        if !bam_file.exists() {
+            Err(anyhow!("BAM file doesn't exists."))
+        } else {
+            self.bam_file = bam_file;
+            Ok(self)
+        }
+    }
+}
+
+impl RunBin for Cramino {
+    fn exec(&self) -> anyhow::Result<()> {
+        if self.result_path.exists() {
+            info!("Result file already exists.");
+            Ok(())
+        } else {
+            let mut args = self.args.clone();
+            args.push(self.bam_file.to_string_lossy().to_string());
+            exec_bin_to_file(&self.prog_path, &args, &self.result_path)
+        }
+    }
+
+    fn parse_results(&mut self) -> anyhow::Result<()> {
+        let file = File::open(&self.result_path)?;
+        let reader = io::BufReader::new(file);
+        let mut lines = reader.lines();
+
+        let mut cramino_res = CraminoRes {
+            file_name: String::new(),
+            number_of_reads: 0,
+            yield_gb: 0.0,
+            mean_coverage: 0.0,
+            n50: 0,
+            median_length: 0.0,
+            mean_length: 0.0,
+            median_identity: 0.0,
+            mean_identity: 0.0,
+            path: String::new(),
+            creation_time: String::new(),
+            checksum: String::new(),
+            normalized_read_count_per_chromosome: HashMap::new(),
+        };
+
+        while let Some(Ok(line)) = lines.next() {
+            if line.starts_with('#') {
+                continue; // Skip the normalized read count header line
+            }
+
+            let parts: Vec<&str> = line.split_whitespace().collect();
+            if parts.len() < 2 {
+                continue; // Skip any malformed lines
+            }
+
+            if !parts[0].starts_with("chr") {
+                match parts[0] {
+                    "File" => cramino_res.file_name = parts[2].to_string(),
+                    "Number" => cramino_res.number_of_reads = parts[3].parse().unwrap_or(0),
+                    "Yield" => cramino_res.yield_gb = parts[2].parse().unwrap_or(0.0),
+                    "N50" => cramino_res.n50 = parts[1].parse().unwrap_or(0),
+                    "Median" => match parts[1] {
+                        "length" => cramino_res.median_length = parts[2].parse().unwrap_or(0.0),
+                        "identity" => cramino_res.median_identity = parts[2].parse().unwrap_or(0.0),
+                        _ => {}
+                    },
+                    "Mean" => match parts[1] {
+                        "coverage" => cramino_res.mean_coverage = parts[2].parse().unwrap_or(0.0),
+                        "length" => cramino_res.mean_length = parts[2].parse().unwrap_or(0.0),
+                        "identity" => cramino_res.mean_identity = parts[2].parse().unwrap_or(0.0),
+                        _ => {}
+                    },
+                    "Path" => cramino_res.path = parts[1].to_string(),
+                    "Creation" => cramino_res.creation_time = parts[2..].join(" "),
+                    "Checksum" => cramino_res.checksum = parts[1].to_string(),
+                    _ => {}
+                }
+            } else {
+                if parts.len() == 2 {
+                    let chromosome = parts[0].to_string();
+                    let count = parts[1].parse().unwrap_or(0.0);
+                    cramino_res
+                        .normalized_read_count_per_chromosome
+                        .insert(chromosome, count);
+                }
+            }
+        }
+
+        self.results = Some(cramino_res);
+        Ok(())
+    }
+
+    fn clean(&self) -> anyhow::Result<()> {
+        if self.remove_result_file {
+            fs::remove_file(&self.result_path)?;
+        }
+        Ok(())
+    }
+}
+
+#[derive(Debug)]
+pub struct CraminoRes {
+    pub file_name: String,
+    pub number_of_reads: u64,
+    pub yield_gb: f64,
+    pub mean_coverage: f64,
+    pub n50: u32,
+    pub median_length: f64,
+    pub mean_length: f64,
+    pub median_identity: f64,
+    pub mean_identity: f64,
+    pub path: String,
+    pub creation_time: String,
+    pub checksum: String,
+    pub normalized_read_count_per_chromosome: HashMap<String, f64>,
+}
+
+impl CraminoRes {
+    pub fn is_woman(&self) -> anyhow::Result<bool> {
+        if let Some(v) = self.normalized_read_count_per_chromosome.get("chrY") {
+            Ok(*v < 0.1)
+        } else {
+            Err(anyhow::anyhow!("Can't get chrY normalized read count."))
+        }
+    }
+}

src/progs/mod.rs

@@ -0,0 +1,3 @@
+
+pub mod cramino;
+

src/utils.rs

@@ -0,0 +1,91 @@
+use std::{fs::File, io::{BufRead, BufReader}, path::PathBuf, process::{Command, Stdio}, time::Instant};
+use anyhow::{Context, Result};
+use log::{info, warn};
+use regex::Regex;
+
+
+pub fn exec_bin(prog_path: &str, args: Vec<String>) -> Result<()> {
+    let start = Instant::now();
+    info!("Spawning {prog_path} with args {}", args.join(", "));
+
+    let mut cmd = Command::new(prog_path)
+        .args(args)
+        .stderr(Stdio::piped())
+        .spawn()
+        .expect("{prog_path} failed to start");
+    
+    let stderr = cmd.stderr.take().unwrap();
+    let reader = BufReader::new(stderr);
+    let re_error = Regex::new(r"(?i)error").unwrap();
+    reader
+        .lines()
+        .filter_map(|line| line.ok())
+        .for_each(|line| {
+            if re_error.is_match(&line) {
+                warn!("{line}");
+            } else {
+                info!("{line}");
+            }
+        });
+    cmd.wait()?;
+
+    let t = start.elapsed();
+    info!("{prog_path} executed in {}s", t.as_secs());
+
+    Ok(())
+}
+
+pub fn exec_bin_to_file(prog_path: &str, args: &Vec<String>, output_file: &PathBuf) -> Result<()> {
+    let start = Instant::now();
+    info!("Spawning {prog_path} with args {}", args.join(", "));
+
+    let out = File::create(output_file).context("failed to open output file")?;
+
+    let mut cmd = Command::new(prog_path)
+        .args(args)
+        .stderr(Stdio::piped())
+        .stdout(out)
+        .spawn()
+        .expect("{prog_path} failed to start");
+    
+    let stderr = cmd.stderr.take().unwrap();
+    let reader = BufReader::new(stderr);
+    let re_error = Regex::new(r"(?i)error").unwrap();
+    reader
+        .lines()
+        .filter_map(|line| line.ok())
+        .for_each(|line| {
+            if re_error.is_match(&line) {
+                warn!("{line}");
+            } else {
+                info!("{line}");
+            }
+        });
+    cmd.wait()?;
+
+    let t = start.elapsed();
+    info!("{prog_path} executed in {}s", t.as_secs());
+
+    Ok(())
+}
+
+
+pub trait RunBin {
+    fn exec(&self) -> Result<()>;
+    fn parse_results(&mut self) -> Result<()>;
+    fn clean(&self) -> Result<()>;
+}
+
+pub trait Run {
+    fn run(&mut self) -> Result<()>;
+}
+
+impl<T> Run for T where T: RunBin {
+    fn run(&mut self) -> Result<()> {
+        self.exec()?;
+        self.parse_results()?;
+        self.clean()?;
+        Ok(())
+    }
+}
+