Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[MRG] speed up SeqToHashes translate #1946

Merged
merged 3 commits into from
Apr 13, 2022
Merged

[MRG] speed up SeqToHashes translate #1946

Changes from 2 commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
335149f
lightning fast translate :zap:
mr-eyes Apr 12, 2022
6f5245b
rust clippy
mr-eyes Apr 12, 2022
671382b
in-line comments for translate
mr-eyes Apr 13, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
37 changes: 21 additions & 16 deletions src/core/src/signature.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@
//!
//! A signature is a collection of sketches for a genomic dataset.

use std::collections::VecDeque;
use std::fs::File;
use std::io;
use std::iter::Iterator;
Expand Down Expand Up @@ -170,7 +169,7 @@ pub struct SeqToHashes {
is_protein: bool,
hash_function: HashFunctions,
seed: u64,
hashes_buffer: VecDeque<u64>,
hashes_buffer: Vec<u64>,

dna_configured: bool,
dna_rc: Vec<u8>,
Expand All @@ -180,6 +179,7 @@ pub struct SeqToHashes {

prot_configured: bool,
aa_seq: Vec<u8>,
translate_iter_step: usize,
}

impl SeqToHashes {
Expand Down Expand Up @@ -215,14 +215,15 @@ impl SeqToHashes {
is_protein,
hash_function,
seed,
hashes_buffer: VecDeque::with_capacity(1000),
hashes_buffer: Vec::with_capacity(1000),
dna_configured: false,
dna_rc: Vec::with_capacity(1000),
dna_ksize: 0,
dna_len: 0,
dna_last_position_check: 0,
prot_configured: false,
aa_seq: Vec::new(),
translate_iter_step: 0,
}
}
}
Expand Down Expand Up @@ -291,18 +292,17 @@ impl Iterator for SeqToHashes {
let hash = crate::_hash_murmur(std::cmp::min(kmer, krc), self.seed);
self.kmer_index += 1;
Some(Ok(hash))
} else if self.hashes_buffer.is_empty() {
} else if self.hashes_buffer.is_empty() && self.translate_iter_step == 0 {
// Processing protein by translating DNA
// TODO: make it a real iterator not a buffer

// Three frames
for i in 0..3 {
for frame_number in 0..3 {
let substr: Vec<u8> = self
.sequence
.iter()
.cloned()
.skip(i)
.take(self.sequence.len() - i)
.skip(frame_number)
.take(self.sequence.len() - frame_number)
.collect();

let aa = to_aa(
Expand All @@ -314,15 +314,15 @@ impl Iterator for SeqToHashes {

aa.windows(self.k_size as usize).for_each(|n| {
let hash = crate::_hash_murmur(n, self.seed);
self.hashes_buffer.push_back(hash);
self.hashes_buffer.push(hash);
});

let rc_substr: Vec<u8> = self
.dna_rc
.iter()
.cloned()
.skip(i)
.take(self.dna_rc.len() - i)
.skip(frame_number)
.take(self.dna_rc.len() - frame_number)
.collect();
let aa_rc = to_aa(
&rc_substr,
Expand All @@ -333,14 +333,19 @@ impl Iterator for SeqToHashes {

aa_rc.windows(self.k_size as usize).for_each(|n| {
let hash = crate::_hash_murmur(n, self.seed);
self.hashes_buffer.push_back(hash);
self.hashes_buffer.push(hash);
});
}
self.kmer_index = self.max_index;
Some(Ok(self.hashes_buffer.remove(0).unwrap()))
Some(Ok(0))
} else {
let first_element: u64 = self.hashes_buffer.pop_front().unwrap();
Some(Ok(first_element))
if self.translate_iter_step == self.hashes_buffer.len() {
self.hashes_buffer.clear();
self.kmer_index = self.max_index;
return Some(Ok(0));
}
let curr_idx = self.translate_iter_step;
self.translate_iter_step += 1;
Some(Ok(self.hashes_buffer[curr_idx]))
}
} else {
// Processing protein
Expand Down