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use crate::clusterer::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.;
let clusters = read_clustering_file(clustering_file);
info!("Read in {} clusters", clusters.len());
debug!("Clusters were: {:#?}", clusters);
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
);
}
}
});
});
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)
}
return all_clusters;
}