IUPACpal

An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre.

IUPACpal is an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences as substrings of a large text, allowing also for potential mismatches and gaps.

Project Structure

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

To run IUPACpal requires the pre-installation of:
- cmake
- C++ compiler
- libdivsufsort (https://github.com/y-256/libdivsufsort)
- sdsl (https://github.com/simongog/sdsl-lite)

To build testing configuration files requires pre-installation of:
- Python (https://www.python.org/)

The necessary files for libdivsufsort and sdsl are already include in this repository.

Installation

Pre-installation of the above tools and libraries may be easily completed by running the following commands on a Ubuntu system within the project directory:

$ sudo apt-get install cmake
$ sudo apt-get install gcc
$ sudo apt-get install python3
$ sudo ./pre-install.sh

The IUPACpal software may then be compiled:

$ make -f Makefile.gcc

This will compile the program for 64-bit integers using the recommended type of Range Minimum Queries (rmq1). This requires double the amount of memory as 32-bit integers.

There are alternative makefiles available in the Makefiles folder, which provide an alternative implementation of Range Minimum Queries (rmq2) and a choice between 32-bit and 64-bit integers .

Running IUPACpal

After compilation the binary file IUPACpal will be created in the working
directory, you may run it within this directory via the command:

$ ./IUPACpal <arguments>

To see the full list of required inputs, run the command with no arguments:

$ ./IUPACpal

Input Parameters

Examples

Example 1

Run on the input file test_data/d00596.fasta with default parameters:

$ ./IUPACpal -f test_data/d00596.fasta

Example 2

Run on the input file test_data/test2.fasta with parameters:
- sequence name in fasta file: seq2
- Maximum permissible gap: 3
- Minimum length: 5
- all other parameters default

$ ./IUPACpal -f test_data/test2.fasta -s seq2 -g 3 -m 5

Example 3

Run on the input file test_data/rand1000000.fasta with parameters:
- Minimum length: 20
- Maximum length: 25
- Maximum permissible gap: 8
- Maximum permissible mismatches: 5
- Output filename: output.txt

$ ./IUPACpal -f test_data/rand1000000.fasta -s seq0 -m 20 -M 25 -g 8 -x 5 -o output.txt

Testing

Automated testing can be performed through the use of timing_tests.sh and a configuration file timing_tests.cfg.

To run the default series of test on IUPACpal, first create the timing_tests.cfg file by running:

$ python3 tools/timing_tests_builder.py

This creates the default configruation file timing_tests.cfg. Testing of IUPACpal can then be performed by running:

$ ./timing_tests.sh

Ensure timing_tests.sh and timing_tests.cfg are in the same directory. To modify the test parameters, you can either directly modify timing_tests.cfg or alternatively modify the Python script tools/timing_tests_builder.py to enable the script to build a different set of tests over the desired range of input parameters.

Test results are written to an output file test_results_<CURRENT_DATE_AND_TIME>.csv.

Author

Steven Watts - steven31415

License

This project is licensed under the GNU GPL License.