nuc-count 0.1.0

NT count test

Just little test to see how fast we can count nucleotides, this optimizes the original code to use SIMD instructions reaching around 15GB/s. For the viral genomes that is around 50k genomes in 0.2s (or 1GB sequences in 0.2 sec). The main speed up actually comes here where we loop 5 times per nucleotide. This seems worse than just saying if nt == a increment count but the branches for this have a huge impact when mis-predicted for each nucleotide.

Usage

If you do not have Cargo yet see here: curl https://sh.rustup.rs -sSf | sh. Then you can install the binary directly using:

cargo install --git ssh://git@github.com/rickbeeloo/viral-nt-counts.git

Then you can run it with:

nuc-count-test --output output.tsv --threads 4 genomes.fasta

Python bindings

Built with maturin (pip install maturin):

maturin develop --release     # into the current venv
maturin build --release       # or a wheel in target/wheels/

The module exposes a single function:

import nuc_count

nuc_count.count("genomes.fasta", "output.tsv", threads=4)  # threads=0 = all cores

It writes the same TSV as the CLI and releases the GIL while counting, so it does not block other Python threads. Errors come back as RuntimeError.

You can increase the threads but if this helps (or harms) mostly depends on the IO speed as the code itself is much faster than the read speed. So likely around 3-4 threads will work best but you can play with it.