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// Copyright 2014-2016 Johannes Köster, Martin Larralde.
// Licensed under the MIT license (http://opensource.org/licenses/MIT)
// This file may not be copied, modified, or distributed
// except according to those terms.
//! One-way open reading frame (ORF) finder algorithm.
//!
//! Complexity: O(n).
//!
//! # Example
//!
//! ```
//! use bio::seq_analysis::orf::{Finder, Orf};
//! let start_codons = vec![b"ATG"];
//! let stop_codons = vec![b"TGA", b"TAG", b"TAA"];
//! let min_len = 50;
//! let finder = Finder::new(start_codons, stop_codons, min_len);
//!
//! let sequence = b"ACGGCTAGAAAAGGCTAGAAAA";
//!
//! for Orf { start, end, offset } in finder.find_all(sequence) {
//! let orf = &sequence[start..end];
//! //...do something with orf sequence...
//! }
//! ```
//!
//! Right now the only way to check the reverse strand for ORF is to use
//! the `alphabet::dna::RevComp` struct and to check for both sequences.
//! But that's not so performance friendly, as the reverse complementation and the ORF research
//! could go on at the same time.
use std::borrow::Borrow;
use std::collections::VecDeque;
use std::iter;
/// An implementation of a naive algorithm finder
// Implementation note:
//
// VecDeque is used rather than the obvious [u8; 3] to represent
// codons because a VecDeque<u8> is used to represent a sliding codon
// (see: State.codon) window which unfortunately, cannot be compared
// to [u8; 3].
#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
pub struct Finder {
start_codons: Vec<VecDeque<u8>>,
stop_codons: Vec<VecDeque<u8>>,
min_len: usize,
}
impl Finder {
/// Create a new instance of a finder for the given start and stop codons and the minimum
/// length of an ORF.
pub fn new<'a>(
start_codons: Vec<&'a [u8; 3]>,
stop_codons: Vec<&'a [u8; 3]>,
min_len: usize,
) -> Self {
Finder {
start_codons: start_codons
.iter()
.map(|x| x.iter().map(|&x| x as u8).collect::<VecDeque<u8>>())
.collect(),
stop_codons: stop_codons
.iter()
.map(|x| x.iter().map(|&x| x as u8).collect::<VecDeque<u8>>())
.collect(),
min_len,
}
}
/// Find all ORFs in the given sequence
pub fn find_all<C, T>(&self, seq: T) -> Matches<'_, C, T::IntoIter>
where
C: Borrow<u8>,
T: IntoIterator<Item = C>,
{
Matches {
finder: self,
state: State::new(),
seq: seq.into_iter().enumerate(),
}
}
}
/// An ORF representation with start and end position of said ORF,
/// as well as offset of the reading frame (1,2,3) and strand location
// (current: +, reverse complementary: -).
#[derive(
Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize,
)]
pub struct Orf {
pub start: usize,
pub end: usize,
pub offset: i8,
}
/// The current algorithm state.
#[derive(Clone, Debug)]
struct State {
start_pos: [Vec<usize>; 3],
codon: VecDeque<u8>,
found: VecDeque<Orf>,
}
impl State {
/// Create new state.
pub fn new() -> Self {
State {
start_pos: [Vec::new(), Vec::new(), Vec::new()],
codon: VecDeque::new(),
found: VecDeque::new(),
}
}
}
/// Iterator over offset, start position, end position and sequence of matched ORFs.
#[derive(Clone, Debug)]
pub struct Matches<'a, C, T>
where
C: Borrow<u8>,
T: Iterator<Item = C>,
{
finder: &'a Finder,
state: State,
seq: iter::Enumerate<T>,
}
impl<'a, C, T> Iterator for Matches<'a, C, T>
where
C: Borrow<u8>,
T: Iterator<Item = C>,
{
type Item = Orf;
fn next(&mut self) -> Option<Orf> {
let mut offset: usize;
// return any orfs already found
if !self.state.found.is_empty() {
return self.state.found.pop_front();
}
for (index, nuc) in self.seq.by_ref() {
// update the codon
if self.state.codon.len() >= 3 {
self.state.codon.pop_front();
}
self.state.codon.push_back(*nuc.borrow());
offset = (index + 1) % 3;
// check if entering orf
if self.finder.start_codons.contains(&self.state.codon) {
self.state.start_pos[offset].push(index);
}
// inside orf
if !self.state.start_pos[offset].is_empty() {
// check if leaving orf
if self.finder.stop_codons.contains(&self.state.codon) {
for start_pos in &self.state.start_pos[offset] {
// check if length is sufficient
if index + 1 - start_pos > self.finder.min_len {
// build results
self.state.found.push_back(Orf {
start: start_pos - 2,
end: index + 1,
offset: offset as i8,
});
// if the first orf is too short, so are the others
} else {
break;
}
}
// reinitialize
self.state.start_pos[offset] = Vec::new();
}
}
if !self.state.found.is_empty() {
return self.state.found.pop_front();
}
}
None
}
}
#[cfg(test)]
mod tests {
use super::*;
fn basic_finder() -> Finder {
let start_codons = vec![b"ATG"];
let stop_codons = vec![b"TGA", b"TAG", b"TAA"];
let min_len = 5;
Finder::new(start_codons, stop_codons, min_len)
}
#[test]
fn test_no_orf() {
let finder = basic_finder();
let sequence = b"ACGGCTAGAAAAGGCTAGAAAA";
assert!(finder.find_all(sequence).next().is_none());
}
#[test]
fn test_one_orf_no_offset() {
let finder = basic_finder();
let sequence = b"GGGATGGGGTGAGGG";
let expected = vec![Orf {
start: 3,
end: 12,
offset: 0,
}];
assert_eq!(expected, finder.find_all(sequence).collect::<Vec<Orf>>());
}
#[test]
fn test_one_orf_with_offset() {
let finder = basic_finder();
let sequence = b"AGGGATGGGGTGAGGG";
let expected = vec![Orf {
start: 4,
end: 13,
offset: 1,
}];
assert_eq!(expected, finder.find_all(sequence).collect::<Vec<Orf>>());
}
#[test]
fn test_two_orfs_different_offsets() {
let finder = basic_finder();
let sequence = b"ATGGGGTGAGGGGGATGGAAAAATAAG";
let expected = vec![
Orf {
start: 0,
end: 9,
offset: 0,
},
Orf {
start: 14,
end: 26,
offset: 2,
},
];
assert_eq!(expected, finder.find_all(sequence).collect::<Vec<Orf>>());
}
#[test]
fn test_three_nested_and_offset_orfs() {
let finder = basic_finder();
let sequence = b"ATGGGGATGGGGGGATGGAAAAATAAGTAG";
let expected = vec![
Orf {
start: 14,
end: 26,
offset: 2,
},
Orf {
start: 0,
end: 30,
offset: 0,
},
Orf {
start: 6,
end: 30,
offset: 0,
},
];
assert_eq!(expected, finder.find_all(sequence).collect::<Vec<Orf>>());
}
}