aaindex (In Development)

Python package for working with AAIndex database (https://www.genome.jp/aaindex/)

AAIndex

Table of Contents

• Introduction
• Requirements
• Installation
• Usage
• Tests
• Contact

Introduction

Requirements

• Python >= 3.6
• numpy >= 1.16.0
• pandas >= 1.1.0
• sklearn >= 0.24
• requests >= 2.24.0

Installation

Install the latest version of aaindex using pip:

pip3 install aaindex

Install by cloning repository:

git clone https://github.com/amckenna41/aaindex.git
python3 setup.py install

Usage

The AAIndex module is made up of the AAIndex class which itself has all the functions/attributes of the package, so when importing the module you have to import the class as well.

from aaindex.aaindex import aaindex

Get record from AAIndex module

The AAIndex class offers diverse functionalities for obtaining any element from any record in the database. Each record is stored in json format in a class attribute called aaindex_json. You can search for a particular record by its index/record code, description or reference. You can also get the index category, and importantly its associated amino acid values.

from aaindex.aaindex import aaindex

full_record = aaindex['CHOP780206']   #get full AAI record
''' Above statement will return -> 
{'description': 'Normalized frequency of N-terminal non helical region (Chou-Fasman, 1978b)', 'notes': '', 'refs': "Chou, P.Y. and Fasman, G.D. 'Prediction of the secondary structure of proteins from their amino acid sequence' Adv. Enzymol. 47, 45-148 (1978); Kawashima, S. and Kanehisa, M.                     'AAindex: amino acid index database.'  Nucleic Acids Res. 28, 374 (2000).", 'values': {'-': 0, 'A': 0.7, 'C': 0.65, 'D': 0.98, 'E': 1.04, 'F': 0.93, 'G': 1.41, 'H': 1.22, 'I': 0.78, 'K': 1.01, 'L': 0.85, 'M': 0.83, 'N': 1.42, 'P': 1.1, 'Q': 0.75, 'R': 0.34, 'S': 1.55, 'T': 1.09, 'V': 0.75, 'W': 0.62, 'Y': 0.99}}
'''
#get individual elements of AAIndex record
record_values = aaindex['CHOP780206']['values']
record_description = aaindex['CHOP780206']['description']
record_references = aaindex['CHOP780206']['refs']

Get category from AAIndex record

"""
Categories: 
Each AAIndex record is classified into 1 of 8 categories: Charge, Composition, Flexibility, Geometry, Hydrophobic, Meta, 
Observable, Polar and Secondary Structure. The record categories are parsed from the aaindex_categories.txt file and can be accessed for each record via the get_category_from_record() function.
"""
category = aaindex.get_category_from_record('CHOP780206')

Get total number of AAIndex records

#get total number of records in AAI database
print(aaindex.get_num_records())

Get list of all AAIndex record names

#get list of all AAIndex record names
print(aaindex.get_record_names())

Directories

• /tests - unit and integration tests for aaindex package.
• /aaindex - source code and all required external data files for package.
• /images - images used throughout README.

Tests

To run all tests, from the main aaindex folder run:

python3 -m unittest discover

To run main test module, from the main aaindex folder run:

python -m unittest tests.test_aaindex -v

Contact

If you have any questions or comments, please contact amckenna41@qub.ac.uk or raise an issue on the Issues tab.

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