Install

This expects you to have python 3 installed on your OS of choice.

Instructions are for Linux/OSX

Running in VirtualEnv

Start a virtual environment:

python3 -m venv venv
source ./venv/bin/activate

Install dependencies

pip install -r requirements.txt

Configuring

Look through the config file: config.conf and edit any settings you like.

Reader

By default, the "fake" reader is configured, which generates random data.

Readers generate one long list of data, that will be handled by the writer.

Input file

Make sure you place the input file in the input folder and configure it in the config.conf

Since the bit reader will literally read bits/bytes, you could use ANY file as input.

(Optional) Generating test data

It's possible to generate (large) datasets for import (on Linux/OSX).

With the example of our large data (155m datapoints), of 2 bits (values of 0-3), we can calulate how many bytes we want the file to be.

155,000k / 8(bits in a byte) * 2(desires bits) = 38,750k

This will take a while as it is generating a file of random content, of 38 megabytes.

dd if=/dev/urandom of=input/test.data bs=1 count=38750000

Running

python3 main.py

You will see output as the file is read in and the PNG is written.

Example output

Step 1 - Reading...
Generating RANDOM data with length 654321 of 2 bits
...  95.0% - 1.03s
Step 1 - Done: Length:  654321
Step 2 - Writing...
Generating PNG - width: 810, height: 808, colors: 5
PNG exported: output/test.png
Step 2 - Done!

Notes

This process can take a while. For the intended purpose (visualizing DNA), it would take about 10 minutes to read in the data and a few more to generate the 12k x 12k image.

However, as far as I can tell, it works just fine!

Nimja/MiniPlot