Module translation 

Amino acid translation tables

This module provides traits for implementing amino acid translation tables.

Enable the translation feature in Cargo.toml:

[dependencies]
bio-seq = { version="0.13", features=["translation"] }

Examples

The standard genetic code is provided as a translation::STANDARD constant:

use bio_seq::prelude::*;
use bio_seq::translation::STANDARD;
use bio_seq::translation::TranslationTable;

let seq = dna!("AATTTGTGGGTTCGTCTGCGGCTCCGCCCTTAGTACTATGAGGACGATCAGCACCATAAGAACAAA");

let aminos: Seq<Amino> = seq
    .windows(3)
    .map(|codon| STANDARD.to_amino(&codon))
    .collect::<Seq<Amino>>();

assert_eq!(
    aminos,
    Seq::<Amino>::try_from("NIFLCVWGGVFSRVSLCARGALSPRAPPLL*SVYTLYM*ERGDTRDISQSAHTPHI*KRENTQK").unwrap()
);

Custom translation tables can be implemented from associative datastructures:

use bio_seq::prelude::*;
use bio_seq::translation::{TranslationTable, TranslationError};

struct Mitochondria;
impl TranslationTable<Dna, Amino> for Mitochondria {
    fn to_amino(&self, codon: &SeqSlice<Dna>) -> Amino {
        if codon == dna!("AGA") {
            Amino::X
        } else if codon == dna!("AGG") {
            Amino::X
        } else if codon == dna!("ATA") {
            Amino::M
       } else if codon == dna!("TGA") {
            Amino::W
        } else {
                Amino::unsafe_from_bits(Into::<u8>::into(codon))
              }
          }

         fn to_codon(&self, _amino: Amino) -> Result<Seq<Dna>, TranslationError> {
              unimplemented!()
          }
      }

       let seq: Seq<Dna> =
           dna!("AATTTGTGGGTTCGTCTGCGGCTCCGCCCTTAGTACTATGAGGACGATCAGCACCATAAGAACAAA").into();
       let aminos: Seq<Amino> = seq
           .windows(3)
           .map(|codon| Mitochondria.to_amino(&codon))
           .collect::<Seq<Amino>>();
       assert_eq!(seq.len() - 2, aminos.len());

       for (x, y) in aminos.into_iter().zip(
           Seq::<Amino>::try_from(
               "NIFLCVWGGVFSRVSLCARGALSPRAPPLL*SVYTLYMWE*GDTRDISQSAHTPHM*K*ENTQK",
           )
           .unwrap()
           .into_iter(),
       ) {
           assert_eq!(x, y)
       }

Errors

Translation tables may not be complete or they may be ambiguous

Structs

CodonTable

A customisable translation table

Enums

TranslationError

Error conditions for codon/amino acid translation

Constants

STANDARD

Traits

PartialTranslationTable

A partial translation table where not all triples of characters map to amino acids

TranslationTable

A codon translation table where all codons map to amino acids