n1chre / bioinf

Project for Bioinformatics course at FER, Zagreb 2016/2017

Fast rank/select operations

Project assignment for Bioinformatics course at University of Zagreb, Faculty of Electrical Engineering and Computing (UNIZG FER), academic year 2016/2017.

Authors

• Filip Hrenić
• Zvonimir Medić
• Matija Oršolić

Implementation

The goal was to implement fast rank/select operations on huge strings (DNA). We accomplished that by using wavelet trees with custom bitset implementation.

Instructions

Getting started

git clone https://github.com/filiphrenic/bioinf
cd bioinf
vagrant up

Use this to clone repository and to setup environment. You don't have to run vagrant up this if you have g++-5, wget and gunzip.

Compilation

bash scripts/compile.sh

Usage

./bioinf [options] input_file
	-o output_file   [default=stdout]
	-c commands_file [default=stdin]
	-w word_size     [default=1024]
	-s               [show statistics]
	-v               [use bool vector instead of bitmask]
	-t               [use red-black tree instead of lookup list]

File structure

Input file must be in FASTA format

Commands look like cmd character index; where cmd is r for rank and s for select. Example would be s A 42 which would return index of 42^nd A.

Example run

./bioinf -c example/cmds_1000_1000.txt -s example/example_1000.fa

Or remove the -c parameter to enter commands directly via keyboard.

To run tests run

./bioinf-test

Create and download files

chmod +x scripts/*
scripts/dl_bacteria.sh
scripts/gen_all.sh

This will download DNA FASTA file of four bacterias into bacterias folder, generate synthetic files of varying lengths (100-1M) into synth folder and generate commands of varying number of commands.

Results

We ran thorough measurements of our implementation on a MacBook Pro 2015 (2,7 GHz Intel Core i5 with 8GB ram) in a virtual machine (Ubuntu 14.04, 4GB RAM, 2 virtual CPU's).

In the next sections we present:

• creation time (time to create data structure)
• running time (time to run a given number of queries on the structure)
• memory consumption (memory used by the process)

note that x-axis has exponential values

Definition:
 * N - input file length
 * W - wavelet size (1024)
 * A - alphabet size (4)
 * B - bitset unit size (64)

Also, let C = N/W (number of wavelets) 

Implementation	Create time	Query time	Memory
Bitset & Lookup	O(C*log(A)*(W+A))	O(W/B*log(C)*log(A))	O(N*log(A))
Bitset & RBTree	O(C*(log(A)*(W+A)+log(C)))	O(W/B*log(C)*log(A))	O(N*log(A))
Vector & Lookup	O(C*log(A)*(W+A))	O(W*log(C)*log(A))	O(N*log(A))
Vector & RBTree	O(C*(log(A)*(W+A)+log(C)))	O(W*log(C)*log(A))	O(N*log(A))

Create time

Run time

Memory consumption

Bacterias

Species	Total length	Create time (milliseconds)	Memory (KB)
Anaplasma_phagocytophilum	1.47M	241	50620
Escherichia_coli	4.64M	769	157780
Mycobacterium_tuberculosis	4.41M	734	149984
Salmonella_enterica	4.95M	814	168260

Run time depends on the number of queries and is similar to example results.

License

MIT License

Copyright (c) 2016 Filip Hrenić, Zvonimir Medić, Matija Oršolić