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use needletail::parse_fastx_file;
use needletail::sequence::Sequence;
#[derive(Debug, PartialEq)]
pub struct GenomeAssemblyStats {
pub num_contigs: usize,
pub num_ambiguous_bases: usize,
pub n50: usize,
}
pub fn calculate_genome_stats(fasta_path: &str) -> GenomeAssemblyStats {
let mut num_contigs = 0;
let mut num_ambiguous = 0;
let mut contig_lengths = vec![];
let mut total_length = 0usize;
let mut reader = parse_fastx_file(fasta_path)
.expect(&format!(
"Failed to calculate genome statistics for file '{}' as there was a problem opening the file",
fasta_path
));
while let Some(seq1) = reader.next() {
let seq = seq1.expect("invalid record");
num_contigs += 1;
let s = seq.sequence();
contig_lengths.push(seq.num_bases());
total_length += seq.num_bases();
for base in s {
if base == &b'N' || base == &b'n' {
num_ambiguous += 1
}
}
}
contig_lengths.sort();
let n50_cutoff = total_length / 2;
let mut n50 = None;
let mut n50_sum = 0usize;
for length in contig_lengths {
n50_sum += length;
if n50_sum >= n50_cutoff {
n50 = Some(length);
break;
}
}
GenomeAssemblyStats {
num_contigs: num_contigs,
num_ambiguous_bases: num_ambiguous,
n50: n50.expect(&format!("Failed to calculate n50 from {}", fasta_path)),
}
}
#[cfg(test)]
mod tests {
use super::*;
fn init() {
let _ = env_logger::builder().is_test(true).try_init();
}
#[test]
fn test_hello_world() {
init();
assert_eq!(
GenomeAssemblyStats {
num_contigs: 161,
num_ambiguous_bases: 6506,
n50: 8289
},
calculate_genome_stats(&"tests/data/abisko4/73.20110600_S2D.10.fna")
)
}
#[test]
fn test_one_contig_n50() {
init();
assert_eq!(
GenomeAssemblyStats {
num_contigs: 1,
num_ambiguous_bases: 0,
n50: 1_000_000
},
calculate_genome_stats(&"tests/data/set1/1mbp.fna")
)
}
}