pandora_lib_assembler/src/lib.rs

pub mod assembler;
pub mod io;

#[cfg(test)]
mod tests {
    use std::path::PathBuf;

    use crate::assembler::{spades::SpadesConfig, wtdbg2::Wtdbg2Config};

    use self::assembler::{assemble_records, flye::FlyeConfig, AssembleConfig};

    use super::*;
    fn init() {
        let _ = env_logger::Builder::from_env(env_logger::Env::default().default_filter_or("info"))
            .is_test(true)
            .try_init();
    }

    #[test]
    fn flye_bam() {
        init();
        let id = "ROBIN";
        let input_id = "143063957-143063957_8a24";

        let res_dir = "/data/longreads_basic_pipe";
        let asm_dir = format!("{res_dir}/{id}/diag/scan/reads/chr9");
        let bam = format!("{asm_dir}/{input_id}.bam");

        let res = assemble_records(
            &PathBuf::from(bam),
            &vec![AssembleConfig::Flye(FlyeConfig::new("/tmp/test_ass_flye"))],
            1
        );
        println!("{res:#?}");
    }

    #[test]
    fn flye_rescue() {
        init();
        let id = "LEVASSEUR";
        let input_id = "12677262-102018167_2c45";
        let chr = "chr10";

        let res_dir = "/data/longreads_basic_pipe";
        let asm_dir = format!("{res_dir}/{id}/diag/scan/reads/{chr}");
        let bam = format!("{asm_dir}/{input_id}.bam");

        let res = assemble_records(
            &PathBuf::from(bam),
            &vec![AssembleConfig::Flye(FlyeConfig::new("/tmp/test_ass_flye"))],
            1
        );
        println!("{res:#?}");
    }

    #[test]
    fn spades_bam() {
        init();
        // let id = "ROBIN";
        // let input_id = "143063957-143063957_8a24";
        // let chr = "chr10";

        let id = "LEVASSEUR";
        let input_id = "12677262-102018167_2c45";
        let chr = "chr10";

        let res_dir = "/data/longreads_basic_pipe";
        let asm_dir = format!("{res_dir}/{id}/diag/scan/reads/{chr}");
        let bam = format!("{asm_dir}/{input_id}.bam");

        let res = assemble_records(
            &PathBuf::from(bam),
            &vec![AssembleConfig::Spades(SpadesConfig::new(
                "/data/spades",
            ))],
            1
        );
        println!("{res:#?}");
    }

    #[test]
    fn wtdbg2_bam() {
        init();
        // let id = "LEVASSEUR";
        // let input_id = "12677262-102018167_2c45";
        // let chr = "chr10";

        let id = "ROBIN";
        let input_id = "143063957-143063957_8a24";
        let chr = "chr9";

        let res_dir = "/data/longreads_basic_pipe";
        let asm_dir = format!("{res_dir}/{id}/diag/scan/reads/{chr}");
        let bam = format!("{asm_dir}/{input_id}.bam");

        let res = assemble_records(
            &PathBuf::from(bam),
            &vec![AssembleConfig::Wtdbg2(Wtdbg2Config::new(
                "/data/wtdbg2",
            ))],
            1
        );
        println!("{res:#?}");
    }
}