AAindex

Installation

Clone the repository

git clone https://github.com/pebonte/AAindex.git

Requirements

1. A Linux/MAC OSX distribution.

2. Install the few required Python packages / modules :

pip install seaborn
pip install scikit_posthocs
pip install pandas
pip install selenium
pip install matplotlib
pip install numpy
pip install scipy

3. A Google chrome webdriver depending on OS.

In the root of the git, a MAC OSX chromedriver is given. You need to download a Linux chromedriver and put it in the root of the git in order to run the program. You can download it here

4. An Internet connection !!!! (all scripts need internet to run).

Run the program

Convert msf files to plain files

Not necessary, data are already retrieved but you can use it to convert msf files to plain files (easy to parse)

cd src
python3 alignment.py
python3 space_to_tab.py

Boxplots and CSV generations

You can test the script with a few data first by only giving 1 index to work on. An example is given. You just need to manually uncomment this line in the script.

#list_aaindex_ids = ['GRAR740102']

To run the script:

cd src
python3 boxplots.py

Statistical tests and heatmaps generation

You can test the script with a few data first by only giving 1 index to work on. An example is given. You just need to manually uncomment this line in the script.

#list_aaindex_ids = ['GRAR740102']

To run the script:

cd src
python3 heatmaps_stats.py

Authors

Master student in bioinformatics at Paris Diderot University.

• Bonté Pierre-Emmanuel