galah 0.5.0

Microbial genome dereplicator
Documentation 
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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)
        .unwrap_or_else(|_| panic!("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
            }
        }
    }

    // Calculate n50
    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_ambiguous_bases: num_ambiguous,
        n50: n50.unwrap_or_else(|| panic!("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")
        )
    }
}