Python BioScience is a package containing different functionalities on different BioScience algorithms. Initially the package will be focused on the Microbiome data analysis, later the functionalities will be expanded to other BioScience tasks.
This module contains different alpha and beta diversity indices to calculate the diversity of a sample and a group of samples. All the indices are discussed in this paper.
Below an example code for finding diversity indices has been shown:
from pybiosci.diversity_indicies import alpha_index
import pandas as pd
df = pd.read_csv('data/simCounts.csv')
print(alpha_index(df, index='Shannon'))
The dataframe is expected to be in a definite format. Row represents the taxa and column represents each sample. Absolute read counts are taken as input and converted to relative abundance when required for an index.