Struct CodonUsage 

pub struct CodonUsage { /* private fields */ }

Codon usage frequency table.

Counts occurrences of each of the 64 codons in a coding sequence.

Implementations

impl CodonUsage

pub fn from_sequence(seq: &[u8]) -> Self

Build a codon usage table from a coding sequence.

The sequence should be in-frame coding DNA/RNA. Non-standard bases and incomplete trailing codons are skipped.

pub fn merge(&mut self, other: &CodonUsage)

Merge another usage table into this one.

pub fn count(&self, codon: &[u8]) -> u64

Raw count for a codon.

pub fn frequency(&self, codon: &[u8]) -> f64

Relative frequency of a codon (count / total codons).

pub fn rscu(&self, codon: &[u8], code: &GeneticCode) -> f64

Relative Synonymous Codon Usage for a codon.

RSCU = observed / expected, where expected = (total for AA) / (number of synonymous codons). An RSCU of 1.0 means no bias.

pub fn relative_adaptiveness(&self, code: &GeneticCode) -> [f64; 64]

Compute the relative adaptiveness (w_i) for all 64 codons.

For each amino acid, w_i = RSCU_i / max(RSCU for that AA). Stop codons get w = 0.0.

Trait Implementations

impl Clone for CodonUsage

fn clone(&self) -> CodonUsage

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for CodonUsage

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.