pandora_lib_variants/src/lib.rs

pub mod annotations;
pub mod callers;
pub mod config;
pub mod in_out;
pub mod sql;
pub mod utils;
pub mod variants;

#[cfg(test)]
mod tests {
    use anyhow::{Ok, Result};
    use indicatif::MultiProgress;
    use indicatif_log_bridge::LogWrapper;
    use noodles_core::{Position, Region};

    use crate::{config::Config, sql::variants_sql::load_variants_name, utils::count_repetitions};

    use super::*;
    #[test]
    fn get_config() -> Result<()> {
        let conf_path = Config::path()?;
        println!("Configuration path {}", conf_path.to_str().unwrap());
        Ok(())
    }

    #[test]
    fn load_from_vcf() -> Result<()> {
        let name = "HATTAB";

        let logger =
            env_logger::Builder::from_env(env_logger::Env::default().default_filter_or("info"))
                .build();
        let multi = MultiProgress::new();
        LogWrapper::new(multi.clone(), logger).try_init().unwrap();

        variants::run_pipe(name, &multi)?;

        Ok(())
    }

    #[test]
    fn load_from_db() -> Result<()> {
        let name = "FAVOT";
        let logger =
            env_logger::Builder::from_env(env_logger::Env::default().default_filter_or("info"))
                .build();
        let multi = MultiProgress::new();
        LogWrapper::new(multi.clone(), logger).try_init().unwrap();

        let mut variants = load_variants_name(name, &multi)?;
        let _variants = variants.get_cat(&variants::VariantCategory::Constit);

        variants.write_vcf_cat("test.vcf.gz", &variants::VariantCategory::Somatic)?;
        println!("{} variants loaded from db.", variants.len());
        Ok(())
    }

    use noodles_fasta::indexed_reader::Builder as FastaBuilder;

    #[test]
    fn check_stretch() -> Result<()> {
        let contig = "chr7";
        let pos = 105303375;

        let cfg = Config::get()?;
        let mut genome_reader = FastaBuilder::default().build_from_path(&cfg.reference_fa)?;
        let start = Position::try_from((pos - 20) as usize).unwrap();
        let end = Position::try_from((pos + 19) as usize).unwrap();
        let r = Region::new(contig.to_string(), start..=end);
        if let std::result::Result::Ok(reg) = genome_reader.query(&r) {
            let seq = String::from_utf8(reg.sequence().as_ref().to_vec()).unwrap();
            let left = &seq[0..20];
            let right = &seq[21..seq.len() - 1];

            let r_plet = count_repetitions(right, 3);

            println!("{left:?}");
            println!("{right:?} {r_plet:?}");
        }

        Ok(())
    }
}