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. Typing iirs --help will return:

Usage: iirs [OPTIONS]

Options:
  -f, --input-file <INPUT_FILE>        Input filename (FASTA) [default: input.fasta]
  -s, --seq-names <SEQ_NAMES>          Input sequence names [default: seq0]
  -m, --min-len <MIN_LEN>              Minimum length [default: 10]
  -M, --max-len <MAX_LEN>              Maximum length [default: 100]
  -g, --max-gap <MAX_GAP>              Maximum permissible gap [default: 100]
  -x, --mismatches <MISMATCHES>        Maximum permissible mismatches [default: 0]
  -o, --output-file <OUTPUT_FILE>      Output filename [default: iirs.out]
  -F, --output-format <OUTPUT_FORMAT>  Output format (classic, csv or custom) [default: classic]
  -q, --quiet                          Quiet flag: Suppresses non-essential output when enabled
  -h, --help                           Print help

With the notable differences being support for multiple sequence names, the ALL_SEQUENCES argument for processing all the sequences in the input file, and the output format. Long versions of the flags are also available.

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

(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=.

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:

cargo build --release --features "parallel tabulation"

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.