pandora_lib_promethion/src/commands/dorado.rs

use std::{
    fs,
    io::{Read, Write},
    path::{Path, PathBuf},
    time::SystemTime,
};

use duct::cmd;
use log::{info, warn};
use uuid::Uuid;

use crate::{config::Config, pod5::FlowCellCase};

pub trait Run {
    fn run(self) -> anyhow::Result<()>;
}

#[derive(Debug, Clone)]
pub struct DoradoParams {
    pub ref_fa: String,
    pub ref_mmi: String,
    pub name: String,
    pub time: String,
    pub pod_dir: String,
    pub samtools_view_threads: u16,
    pub samtools_sort_threads: u16,
}

pub struct Dorado {
    config: Config,
    case: FlowCellCase,
    case_dir: String,
    time_dir: String,
    bam: String,
    start_time: SystemTime,
    end_time: SystemTime,
    is_done: bool,
    log: Vec<String>,
}

impl Dorado {
    pub fn init(case: FlowCellCase, config: Config) -> anyhow::Result<Self> {
        let data_dir = "/data/longreads_basic_pipe";
        let case_dir = format!("{}/{}", data_dir, case.id);
        let time_dir = format!("{}/{}", case_dir, case.time_point);
        let bam = format!("{}/{}_{}_hs1.bam", time_dir, case.id, case.time_point);

        Ok(Self {
            config,
            start_time: SystemTime::now(),
            end_time: SystemTime::now(),
            is_done: false,
            log: Vec::new(),
            case_dir,
            time_dir,
            bam,
            case,
        })
    }
    fn create_reference_mmi(&self) -> anyhow::Result<()> {
        if !std::path::Path::new(&self.config.align.ref_mmi).exists() {
            cmd!(
                "minimap2",
                "-x",
                "map-ont",
                "-d",
                &self.config.align.ref_mmi,
                &self.config.align.ref_fa
            )
            .run()?;
        }
        Ok(())
    }

    fn create_directories(&self) -> anyhow::Result<()> {
        if !std::path::Path::new(&self.case_dir).exists() {
            fs::create_dir(&self.case_dir)?;
        }
        if !std::path::Path::new(&self.time_dir).exists() {
            fs::create_dir(&self.time_dir)?;
        }
        Ok(())
    }

    fn basecall_align(&mut self, dorado_bin: &str) -> anyhow::Result<()> {
        let pod_dir = &self.case.pod_dir.display();
        let ref_mmi = &self.config.align.ref_mmi;
        let bam = &self.bam;
        let samtools_view_threads = self.config.align.samtools_view_threads;
        let samtools_sort_threads = self.config.align.samtools_sort_threads;

        let dorado = format!(
            "{dorado_bin} basecaller sup,5mC_5hmC {pod_dir} --trim all --reference {ref_mmi}"
        );
        let samtools_view = format!("samtools view -h -@ {samtools_view_threads} -b /dev/stdin");
        let samtools_sort = format!("samtools sort -@ {samtools_sort_threads} /dev/stdin -o {bam}");
        let pipe = format!("{dorado} | {samtools_view} | {samtools_sort}");
        info!("Running: {pipe}");

        let pipe_cmd = cmd!("bash", "-c", pipe);
        let mut reader = pipe_cmd.stdout_capture().reader()?;

        let mut buffer = [0; 1];
        let mut line = String::new();

        loop {
            match reader.read(&mut buffer) {
                Ok(0) => break, // End of output
                Ok(_) => {
                    let char = buffer[0] as char;
                    eprint!("{}", char);
                    std::io::stderr().flush()?;

                    if char == '\n' {
                        // Send the complete line
                        self.log.push(line.clone());
                        line.clear();
                    } else {
                        line.push(char);
                    }
                }
                Err(err) => {
                    warn!("Error reading from stderr: {}", err);
                    break;
                }
            }
        }

        Ok(())
    }

    pub fn index(&self) -> anyhow::Result<()> {
        let t = self.config.align.samtools_view_threads.to_string();
        let cmd = format!("index -@ {t} {}", &self.bam);
        info!("Running  samtools {cmd}");
        cmd!("samtools", "index", "-@", &t, &self.bam).run()?;
        Ok(())
    }

    fn run_cramino(&self) -> anyhow::Result<()> {
        let cramino_out = format!(
            "{}/{}_{}_hs1_cramino.txt",
            self.time_dir, self.case.id, self.case.time_point
        );
        // if !Path::new(&cramino_out).exists() {
        info!("Quality control of BAM: {}", self.bam);
        let output = duct::cmd!(
            "cramino",
            "-t",
            "150",
            "--hist",
            "--checksum",
            "--karyotype",
            &self.bam
        )
        .stdout_capture()
        .unchecked()
        .run()?;

        fs::write(cramino_out, output.stdout)?;
        // }
        Ok(())
    }

    fn run_modkit(&self) -> anyhow::Result<()> {
        let mod_summary = format!(
            "{}/{}_{}_5mC_5hmC_summary.txt",
            self.time_dir, self.case.id, self.case.time_point
        );
        // if !Path::new(&mod_summary).exists() {
        info!("Generating base modification summary for BAM: {}", self.bam);
        let output = cmd!("modkit", "summary", "-t", "50", &self.bam)
            .stdout_capture()
            .unchecked()
            .run()?;

        fs::write(mod_summary, output.stdout)?;
        // }
        Ok(())
    }

    fn create_fastq(&self) -> anyhow::Result<()> {
        let bam = &self.bam;
        let fastq = format!(
            "{}/{}/{}/{}_{}.fastq.gz",
            self.case_dir, self.case.id, self.case.time_point, self.case.id, self.case.time_point
        );
        if !std::path::Path::new(&fastq).exists() {
            let samtools = format!("samtools fastq -@ 150 {bam}");
            let crabz = format!("crabz -f bgzf - -o {fastq}");
            let pipe = format!("{samtools} | {crabz}");
            info!("Running: {pipe}");
            let pipe_cmd = duct::cmd!("bash", "-c", pipe);
            pipe_cmd.run()?;
        }
        Ok(())
    }

    fn merge_bam(&self, bam: &Path) -> anyhow::Result<()> {
        let into = PathBuf::from(&self.bam);
        let dir = into.parent().unwrap();

        let original_file = into.file_name().unwrap().to_string_lossy().to_string();
        let original_i = dir.join(format!("{original_file}.bai"));
        if !original_i.exists() {
            self.index()?;
        }

        let tmp_original_file = format!("{}.bam", Uuid::new_v4());
        let tmp_original = dir.join(tmp_original_file.clone());
        let tmp_original_i = dir.join(format!("{tmp_original_file}.bai"));

        info!("Moving {} to {}", &into.display(), &tmp_original.display());
        fs::rename(&into, &tmp_original)?;
        info!(
            "Moving {} to {}",
            &original_i.display(),
            &tmp_original_i.display()
        );
        fs::rename(original_i, tmp_original_i.clone())?;

        let cmd = format!(
            "samtools merge -@ 160 -h {} {} {} {}",
            bam.display(),
            into.display(),
            bam.display(),
            tmp_original.display()
        );
        info!("Running {cmd}");
        cmd!(
            "samtools",
            "merge",
            "-@",
            "160",
            "-h",
            bam,
            into,
            bam,
            tmp_original.clone()
        )
        .run()?;
        fs::remove_file(tmp_original)?;
        fs::remove_file(tmp_original_i)?;
        self.index()?;
        Ok(())
    }

    pub fn from_mux(cases: Vec<FlowCellCase>, config: Config) -> anyhow::Result<()> {
        // Creating a temporary directory
        let tmp_dir = format!("{}/.{}", config.result_dir, Uuid::new_v4());
        info!("Creating tmp dir {tmp_dir}");
        fs::create_dir(&tmp_dir)?;

        // Dorado base calling and align into a temporary bam file
        let muxed_bam = format!("{tmp_dir}/muxed.bam");
        let dorado_bin = &config.align.dorado_bin;
        let dorado_arg = &config.align.dorado_basecall_arg;
        let pod_dir = cases[0].pod_dir.display();
        let ref_mmi = &config.align.ref_mmi;
        let samtools_view_threads = config.align.samtools_view_threads;

        let dorado = format!(
            "{dorado_bin} basecaller {dorado_arg} {pod_dir} --trim all --reference {ref_mmi}"
        );
        let samtools_view =
            format!("samtools view -h -@ {samtools_view_threads} -b -o {muxed_bam}");
        let pipe = format!("{dorado} | {samtools_view}");
        info!("Running: {pipe}");
        let pipe_cmd = cmd!("bash", "-c", pipe);
        pipe_cmd.run()?;

        info!("Basecalling ✅");

        // Demux the temporary bam file
        // Get the sequencing kit from the first pod5 file
        let muxed_pod_dir = &cases.first().unwrap().pod_dir;
        let pod_path = fs::read_dir(muxed_pod_dir)?
            .filter_map(|p| p.ok())
            .map(|p| p.path())
            .filter(|p| p.extension().unwrap() == "pod5")
            .take(1)
            .collect::<Vec<PathBuf>>()
            .pop()
            .unwrap();
        let sequencing_kit = pandora_lib_pod5::Pod5Info::from_pod5(pod_path.to_str().unwrap())
            .sequencing_kit
            .to_uppercase();

        let tmp_demux_dir = format!("{tmp_dir}/demuxed");
        fs::create_dir(&tmp_demux_dir)?;

        info!("Demux from {sequencing_kit} into {tmp_demux_dir}",);

        duct::cmd!(
            &config.align.dorado_bin,
            "demux",
            "--output-dir",
            &tmp_demux_dir,
            "--kit-name",
            &sequencing_kit,
            &tmp_dir,
        )
        .run()?;
        info!("Demux ✅");

        for case in cases.iter() {
            let bam = format!(
                "{tmp_demux_dir}/{sequencing_kit}_barcode{}.bam",
                case.barcode
            );

            // Trim
            let trimmed_bam = format!(
                "{tmp_demux_dir}/{sequencing_kit}_barcode{}_trimmed.bam",
                case.barcode
            );
            let pipe = format!(
                "{} trim {bam} | samtools view -h -@ {} -b /dev/stdin -o {trimmed_bam}",
                config.align.dorado_bin, &config.align.samtools_view_threads
            );
            cmd!("bash", "-c", pipe).run()?;

            // Align
            let aligned_bam = format!(
                "{tmp_demux_dir}/{sequencing_kit}_barcode{}_aligned.bam",
                case.barcode
            );
            let dorado = format!(
                "{} aligner --threads 160 {} {trimmed_bam}",
                config.align.dorado_bin, config.align.ref_fa,
            );
            let samtools_view = format!(
                "samtools view -h -@ {} -b /dev/stdin",
                &config.align.samtools_view_threads
            );
            let samtools_sort = format!(
                "samtools sort -@ {} /dev/stdin -o {aligned_bam}",
                &config.align.samtools_sort_threads
            );
            let pipe = format!("{dorado} | {samtools_view} | {samtools_sort}");
            info!("Running {pipe}");

            cmd!("bash", "-c", pipe).run()?;

            let d = Dorado::init(case.clone(), config.clone())?;
            d.create_directories()?;

            if PathBuf::from(&d.bam).exists() {
                info!("merge");
                d.merge_bam(&PathBuf::from(aligned_bam))?;
            } else {
                info!("Moving from {} to {}", bam, d.bam);
                fs::rename(aligned_bam, d.bam.clone())?;
                d.index()?;
            }

            d.run_cramino()?;
            d.run_modkit()?;
        }
        fs::remove_dir(tmp_dir)?;

        Ok(())
    }

    pub fn run_pipe(&mut self) -> anyhow::Result<()> {
        let start_time = std::time::SystemTime::now();
        self.start_time = start_time;

        info!("Running Dorado with params: {:#?}", self.config);

        let dorado_bin = "/data/tools/dorado-0.7.2-linux-x64/bin/dorado";

        self.create_reference_mmi()?;
        self.create_directories()?;

        info!(
            "Reading {} pod5 from: {}",
            self.case.time_point, self.config.pod_dir
        );
        let bam_path = std::path::Path::new(&self.bam);

        if !bam_path.exists() {
            self.basecall_align(dorado_bin)?;
        } else {
            let new_bam_path = bam_path
                .parent()
                .unwrap()
                .join(format!("{}.bam", Uuid::new_v4()));
            warn!("Creating new bam {}", new_bam_path.display());

            self.basecall_align(dorado_bin)?;
            self.merge_bam(&new_bam_path)?;
        }

        self.run_cramino()?;
        self.run_modkit()?;
        self.create_fastq()?;

        let end_time = std::time::SystemTime::now();
        self.end_time = end_time;
        let execution_time = end_time.duration_since(start_time).unwrap().as_secs_f64();
        info!(
            "Dorado and Minimap2 execution time: {} seconds",
            execution_time
        );
        self.is_done = true;

        Ok(())
    }
}