galah 0.5.0

Microbial genome dereplicator
Documentation 
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use crate::fastani::calculate_fastani;
use std;
use std::process;

use rayon::prelude::*;

pub fn validate_clusters(
    clustering_file: &str,
    ani_threshold: f32,
    fastani_min_aligned_threshold: f32,
    fastani_fraglen: u32,
) {
    let ani = ani_threshold * 100.;

    // Read cluster file
    let clusters = read_clustering_file(clustering_file);
    info!("Read in {} clusters", clusters.len());
    debug!("Clusters were: {:#?}", clusters);

    // FastANI within each cluster - each should be within the threshold
    clusters.par_iter().for_each(|cluster| {
        let rep = &cluster[0];
        cluster.par_iter().for_each(|genome| {
            let fastani_res =
                calculate_fastani(rep, genome, fastani_min_aligned_threshold, fastani_fraglen);
            match fastani_res {
                Some(fastani) => {
                    if fastani >= ani {
                        debug!("FastANI between {} and {} is ok: {}", rep, genome, fastani);
                    } else {
                        error!(
                            "FastANI between {} and {} is not ok: {}",
                            rep, genome, fastani
                        );
                    }
                }
                None => {
                    error!(
                        "FastANI between {} and {} is not ok: fastani was too divergent",
                        rep, genome
                    );
                }
            }
        });
    });

    // FastANI between each representative - each should be further than the ANI
    let reps: Vec<&str> = clusters.iter().map(|c| c[0].as_str()).collect();
    reps.par_iter().enumerate().for_each(|(i, rep1)| {
        reps.par_iter().enumerate().for_each(|(j, rep2)| {
            if i < j {
                let fastani_res =
                    calculate_fastani(rep1, rep2, fastani_min_aligned_threshold, fastani_fraglen);
                match fastani_res {
                    Some(fastani) => {
                        if fastani < ani {
                            debug!(
                                "FastANI between reps {} and {} is ok: {}",
                                rep1, rep2, fastani
                            );
                        } else {
                            error!(
                                "FastANI between reps {} and {} is not ok: {}",
                                rep1, rep2, fastani
                            );
                        }
                    }
                    None => {
                        debug!(
                            "FastANI between reps {} and {} is ok: fastani was too divergent",
                            rep1, rep2
                        );
                    }
                }
            }
        });
    });
}

fn read_clustering_file(clustering_file: &str) -> Vec<Vec<String>> {
    let mut rdr = csv::ReaderBuilder::new()
        .delimiter(b'\t')
        .has_headers(false)
        .from_reader(std::fs::File::open(clustering_file).expect("Failed to open clustering file"));

    let mut current_cluster_rep: Option<String> = None;
    let mut all_clusters = vec![];
    let mut current_cluster = vec![];

    for record_res in rdr.records() {
        let record = record_res.expect("Failed to parse clustering file.");
        if record.len() != 2 {
            error!(
                "Unexpectedly didn't find exactly 2 fields in clustering file: {:?}",
                record
            );
            process::exit(1);
        }

        if record[0] == record[1] {
            if current_cluster_rep.is_some() {
                all_clusters.push(current_cluster)
            }
            current_cluster = vec![];
            current_cluster_rep = Some(record[0].to_string());
        }
        current_cluster.push(record[1].to_string());
    }
    if current_cluster_rep.is_some() {
        all_clusters.push(current_cluster)
    }
    all_clusters
}