iirs

IIRS is an Iupac Inverted RepeatS finder written in rust (rs), ported from IUPACpal, result of this paper.

That is, an exact tool for efficient identification of Inverted Repeats (IRs) in IUPAC-encoded DNA sequences as substrings of a large text, allowing also for potential mismatches and gaps.

Compared to the original, this version is faster, platform-independent and modular, facilitating the creation of customized format outputs. It does not require cmake nor sdsl. It uses divsufsort instead of libdivsufsort.

How to use the binary

The command line shares much of the functionality of the original IUPACpal.

Type iirs --help for a full description.

The notable differences are:

• Support for multiple sequence names.
• ALL_SEQUENCES argument for processing all the sequences in the input file.
• Output format.

iirs -f input.fasta -s 't1 t2' -g 5 -F csv
iirs -f input.fasta --seq-names t1 --max-gap 5 --output-format csv
iirs -f input.fasta -s ALL_SEQUENCES -g 5 -m 3 -F csv

Many more practical examples can be found in the justfile.

How to install the binary

You can either build from source:

$ cargo install iirs

Or download the latest binary from releases and extract it somewhere on your $PATH.

Features

The default uses a Sparse Table implementation for the range minimum query, and it is sequential over IR centers. To change this behaviour you can use the features tabulation, parallel or a combination of both. This may result in a significant speed increase:

cargo install iirs --features "parallel tabulation"

Extra

It can also be used as a library both in rust and python.

cargo add iirs [--features X]

Or to python, after cloning the repo, via (no wheels yet):

pip install py-iirs/

Both libraries are minimal and only contain a struct / class SearchParams that does some bound checking, and a find_irs function.

Testing

• cargo test for unit tests.
• Justfile for individual tests against sequences. Some use the Linux profiler perf. To see the full list of commands use just -l.
• bench.rs benches against a single file. To use together with just bench after modifying the parameters in bench.rs. To test against different features you can add them as arguments: just bench parallel or just bench parallel tabulation.
• logs.rs benches against the cpp binary. You will need a IUPACpal binary (and they only support Linux). The binary is expected to be in the bench folder, but that can be changed in logs.rs and validate.py.
• Note that just heatmap requires the python libraries listed in bench/requirements.txt.