iirs

IIRS is an Iupac Inverted RepeatS finder written in rust (rs).

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.

This is a port of IUPACpal, result of their work on this paper.

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

How to use

TODO - but mainly it works much like the original with an extra flag for the type of output format.

There are many examples in the justfile.

This also works as a library: The find_irs function is exported (think of crates.io).

How to install

(Option 1) Download executable

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

(Option 2) Build executable

$ git clone https://github.com/daxida/iirs
$ cd iirs
$ cargo build --release
$ // The binary will be located at `target/release/iirs`

(Option 3) Build from source:

$ git clone https://github.com/daxida/iirs
$ cargo install --path=.

Branches

TODO

• master (Sparse table)
• parallel (parallelize the main loop - not ideal if we want to parallelize over sequences, but THE FASTEST if we only query one sequence)
• tabulation (maybe better than master? needs testing)
• visualize && custom > ignore

Testing

• cargo test for unit tests.
• Justfile for individual tests against sequences. Some use the Linux profiler perf.
• bench.rs benches against a single file. To use together with just bench after modifying the parameters in bench.rs.
• 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.
• For instance, create the heatmaps with just printlogs. You can also modify the steps in which the binaries are compared. A heatmap will be created per size_seq (size of sequence). NOTE: There is a requirements.txt that needs to be previously installed, with libraries like plotly to be able to print the heatmaps.

Links

• IUPACpal
• divsufsort and dismantling divsufsort
• libdivsufsort port in rust
• Alternative RMQ implementations