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// Copyright 2014-2015 Johannes Köster, Peer Aramillo Irizar.
// Licensed under the MIT license (http://opensource.org/licenses/MIT)
// This file may not be copied, modified, or distributed
// except according to those terms.
//! Implementation of the DNA alphabet.
//!
//! # Example
//!
//! ```
//! use bio::alphabets;
//! let alphabet = alphabets::dna::alphabet();
//! assert!(alphabet.is_word(b"GATTACA"));
//! assert!(alphabet.is_word(b"gattaca"));
//! assert!(!alphabet.is_word(b"ACGU"));
//! ```
use std::borrow::Borrow;
use crate::alphabets::Alphabet;
/// The DNA alphabet (uppercase and lowercase).
pub fn alphabet() -> Alphabet {
Alphabet::new(b"ACGTacgt")
}
/// The DNA alphabet including N (uppercase and lowercase).
pub fn n_alphabet() -> Alphabet {
Alphabet::new(b"ACGTNacgtn")
}
/// The IUPAC DNA alphabet (uppercase and lowercase).
pub fn iupac_alphabet() -> Alphabet {
Alphabet::new(b"ACGTRYSWKMBDHVNZacgtryswkmbdhvnz")
}
lazy_static! {
static ref COMPLEMENT: [u8; 256] = {
let mut comp = [0; 256];
for (v, a) in comp.iter_mut().enumerate() {
*a = v as u8;
}
for (&a, &b) in b"AGCTYRWSKMDVHBN".iter().zip(b"TCGARYWSMKHBDVN".iter()) {
comp[a as usize] = b;
comp[a as usize + 32] = b + 32; // lowercase variants
}
comp
};
}
/// Return complement of given DNA alphabet character (IUPAC alphabet supported).
///
/// Casing of input character is preserved, e.g. `t` → `a`, but `T` → `A`.
/// All `N`s remain as they are.
///
/// ```
/// use bio::alphabets::dna;
///
/// assert_eq!(dna::complement(65), 84); // A → T
/// assert_eq!(dna::complement(99), 103); // c → g
/// assert_eq!(dna::complement(78), 78); // N → N
/// assert_eq!(dna::complement(89), 82); // Y → R
/// assert_eq!(dna::complement(115), 115); // s → s
/// ```
#[inline]
pub fn complement(a: u8) -> u8 {
COMPLEMENT[a as usize]
}
/// Calculate reverse complement of given text (IUPAC alphabet supported).
///
/// Casing of characters is preserved, e.g. `b"NaCgT"` → `b"aCgTN"`.
/// All `N`s remain as they are.
///
/// ```
/// use bio::alphabets::dna;
///
/// assert_eq!(dna::revcomp(b"ACGTN"), b"NACGT");
/// assert_eq!(dna::revcomp(b"GaTtaCA"), b"TGtaAtC");
/// assert_eq!(dna::revcomp(b"AGCTYRWSKMDVHBN"), b"NVDBHKMSWYRAGCT");
/// ```
pub fn revcomp<C, T>(text: T) -> Vec<u8>
where
C: Borrow<u8>,
T: IntoIterator<Item = C>,
T::IntoIter: DoubleEndedIterator,
{
text.into_iter()
.rev()
.map(|a| complement(*a.borrow()))
.collect()
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn is_word() {
assert!(alphabet().is_word(b"GATTACA"));
}
#[test]
fn is_no_word() {
assert!(!alphabet().is_word(b"gaUUaca"));
}
#[test]
fn symbol_is_no_word() {
assert!(!alphabet().is_word(b"#"));
}
#[test]
fn number_is_no_word() {
assert!(!alphabet().is_word(b"42"));
}
}