pandora_lib_promethion/src/annotation/echtvar.rs

use std::path::{Path, PathBuf};

use anyhow::{Ok, Result};
use uuid::Uuid;

use crate::{
    commands::{
        CapturedOutput, Command as JobCommand, LocalBatchRunner, LocalRunner, SbatchRunner,
        SlurmParams, SlurmRunner,
    },
    config::Config,
    run,
};

use super::{cosmic::Cosmic, gnomad::GnomAD};

pub struct EchtvarJob {
    pub input_vcf: PathBuf,
    pub output_vcf: PathBuf,
    pub config: Config,
}

impl JobCommand for EchtvarJob {
    fn cmd(&self) -> String {
        let sources = self
            .config
            .echtvar_sources
            .iter()
            .map(|e| format!("-e {e}"))
            .collect::<Vec<String>>()
            .join(" ");
        format!(
            "{echtvar_bin} anno {sources} {input_vcf} {output_vcf}",
            echtvar_bin = self.config.echtvar_bin,
            sources = sources,
            input_vcf = self.input_vcf.display(),
            output_vcf = self.output_vcf.display()
        )
    }
}
impl LocalRunner for EchtvarJob {}
impl LocalBatchRunner for EchtvarJob {}

impl SlurmRunner for EchtvarJob {
    fn slurm_args(&self) -> Vec<String> {
        SlurmParams {
            job_name: Some(format!("echtvar_{}", Uuid::new_v4())),
            cpus_per_task: Some(1),
            mem: Some("20G".into()),
            partition: Some("shortq".into()),
            gres: None,
        }
        .to_args()
    }
}

impl SbatchRunner for EchtvarJob {
    fn slurm_params(&self) -> SlurmParams {
        SlurmParams {
            job_name: Some(format!("echtvar_{}", Uuid::new_v4())),
            cpus_per_task: Some(1),
            mem: Some("20G".into()),
            partition: Some("shortq".into()),
            gres: None,
        }
    }
}

pub fn run_echtvar(
    in_path: impl AsRef<Path>,
    output_vcf: impl AsRef<Path>,
    config: &Config,
) -> Result<CapturedOutput> {
    let mut job = EchtvarJob {
        input_vcf: in_path.as_ref().into(),
        output_vcf: output_vcf.as_ref().into(),
        config: config.clone(),
    };
    run!(config, &mut job)
}

pub fn parse_echtvar_val(s: &str) -> Result<(Option<Cosmic>, Option<GnomAD>)> {
    let mut cosmic_parts = Vec::new();
    let mut gnomad_parts = Vec::new();

    for part in s.split(';').map(str::trim).filter(|p| !p.is_empty()) {
        if part.starts_with("gnomad_") {
            gnomad_parts.push(part);
        } else {
            cosmic_parts.push(part);
        }
    }

    // COSMIC: missing if CNT is absent or CNT is -1 or MISSING
    let cosmic = {
        let cnt = cosmic_parts.iter().find(|p| p.starts_with("CNT=")).copied();
        match cnt {
            Some("CNT=-1") | Some("CNT=MISSING") | None => None,
            Some(_) => Some(cosmic_parts.join(";").parse::<Cosmic>()?),
        }
    };

    // gnomAD: your choice; this keeps your "all -1 => None" behavior
    let gnomad = if gnomad_parts.is_empty() || gnomad_parts.iter().all(|p| p.ends_with("=-1")) {
        None
    } else {
        Some(gnomad_parts.join(";").parse::<GnomAD>()?)
    };

    Ok((cosmic, gnomad))
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::{
        annotation::{Annotation, Annotations, Caller, Sample},
        helpers::test_init,
        variant::{variant_collection::ExternalAnnotation, vcf_variant::VcfVariant},
    };

    #[test]
    fn echtvar_parse() -> anyhow::Result<()> {
        test_init();

        let s = "gnomad_ac=1;gnomad_an=-1;gnomad_af=-1;gnomad_af_oth=-1;gnomad_af_ami=-1;gnomad_af_sas=-1;gnomad_af_fin=-1;gnomad_af_eas=-1;gnomad_af_amr=-1;gnomad_af_afr=-1;gnomad_af_mid=-1;gnomad_af_asj=-1;gnomad_af_nfe=-1;CNT=188";
        let (cosmic, _gnomad) = parse_echtvar_val(s)?;

        println!("{cosmic:#?}");

        Ok(())
    }

    #[test]
    fn echtvar_run() -> anyhow::Result<()> {
        test_init();
        let config = Config::default();

        let variants: Vec<VcfVariant> = vec![
            "chr12\t25116560\t.\tC\tG\t18.2\tPASS\t.\tGT:GQ:DP:AD:VAF:PL\t1/1:18:45:37,7:0.155556:18,25,0".parse()?,
            "chr1\t5619\trs1470452993\tA\tC \t.\tPASS\t.\t.\t.".parse()?
        ];

        let annotations = Annotations::default();

        let caller = Annotation::Callers(Caller::ClairS, Sample::Somatic);

        variants.iter().for_each(|v| {
            annotations.insert_update(v.hash(), std::slice::from_ref(&caller));
        });

        let ext_annot = ExternalAnnotation::init("TEST", &config)?;
        ext_annot.annotate(&variants, &annotations)?;

        println!("{annotations:#?}");

        Ok(())
    }
}