curatedmetagenomicdata3 0.1.4

Python wrapper for curatedMetagenomicData3.

# curatedMetagenomicData3-python

Python Wrapper for curatedMetagenomicData3

# Installation

This package has been tested on python-3.7+. You can install it from PyPi[https://pypi.org/project/curatedmetagenomicdata3/]:

pip install curatedmetagenomicdata3

# Usage

See demo.py for a full working demo. You can follow along the below in a IPython terminal or Jupyter notebook

## Pre-requisites

# Decide on a folder to store files in # This package downloads files containing raw annotation data based on your queries

import curatedmetagenomicdata3 as cmd3 source_dir = “test” # This folder needs to exist beforehand

## 1) Open Metadata

# This function returns a DataFrame containing all sample metadata df = cmd3.get_metadata()

## 2) Decide What Samples You Want Annotations for

# For example, let’s say you want to download taxonomic relative # abundances data for all samples for Type 2 Diabetes patients

t2d = df[df[‘disease’] == ‘T2D’]

## 3) Compile OTU Data for Chosen Samples

# Taxonomic Relative Abundances taxa = cmd3.assemble_taxa_dataset(t2d, source_dir)

That’s it! taxa will be a dataframe containing the relative abundances data for the samples you chose. All of the data for that will be downloaded and cached to source_dir automatically for future use.

You can also get pathway abundances as well

# Pathway Relative Abundances pathways = cmd3.assemble_pathways_dataset(t2d, source_dir)