Project Overview and Instructions

Project Structure:

The project structure before running any of the installations or the library is as follows.

BIOIT/
  ├── logic/
  │     └──  meme.py # Function to run MEME
  ├── results/ # Output results
  │     ├── meme_output/ # MEME results
  │     └── visuals_output/ # Visualizations
  ├── visuals/
  │     └──  visualizations.py # Generating and saving visualizations
  ├── meme-5.4.1/  # NOTE- this is the tool, which should be downloaded below. It is not included in the project.
  ├── dna.file # DNA file created by
  ├── main.py # Main entry point
  └── README.md # Instructions

The uploaded project however, has additional folders and files, which are the result of running the installments needed for the project.

Installing dependencies:

First, make sure that you have downloaded the necessary libraries to run the project. This project is run on Python 3.9.21.

The neccessary libraries that should be downloaded are:

requests, wget, libxml2, libxslt, zlib

If the libraries are not previously installed, follow these steps, or modify according to local setup. Homebrew and Pip was used here.

pip install requests

brew install wget

brew install libxml2

brew install libxslt

brew install zlib

wget http://meme-suite.org/meme-software/5.4.1/meme-5.4.1.tar.gz

tar -zxvf meme-5.4.1.tar.gz

At this point a new file called meme-5.4.1.tar.gz should be created, as well as a folder called meme-5.4.1. These files are quite large, and I´m unable to upload them without using Git Large File Storage, so the best way to use and create them is to do it locally, using the steps described. After unpacking the tar file, and successfully using the meme-5.4.1 folder, the tar file(not the meme folder) can be deleted, as it is only necessary before unpacking it and creating the meme-5.4.1 folder.


cd meme-5.4.1

./configure

make

sudo make install

meme -version

At this point you should have configured meme-5.4.1 correctly, and if all is correctly installed the meme-version should be meme-5.4.1 upon running the last command.

For the visualizations:

Make sure you have Pillow, Ghostscript and mathplotlib downloaded. If not:

pip install matplotlib 

pip install pillow

brew install ghostscript

Running the project:

After downloading meme, as per the instructions above, run:

python main.py

This will fetch and create the dna sequence files, run MEME and the visualizations. All results can be found in /results.

Project Delivery Explanation

In this github account I have published a successfull run, with all created files. If one was to want to recreate this from scratch, one should remove all the results and working files, that is:

Remove:

dna.file
results/ (Only the content of the folder - it is very important to leave the actual folder called "results")

NB: If you change the values for the meme finder motifs, eg from 3 to 4, make sure to change or block out the visualizations code, as this is set up to find only three motifs.

Video

The video is uploaded here in the code base, but also on https://youtu.be/L8ezayjS_fY

eastautl/MOL3022

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