Python wrapper for curatedMetagenomicData3.
Project description
# curatedMetagenomicData3-python
Python Wrapper for curatedMetagenomicData3
# Installation
pip install curatedmetagenomicdata3
# Usage
## 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”
## 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 = 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 = assemble_pathways_dataset(t2d, source_dir)
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Hashes for curatedmetagenomicdata3-0.1.2.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 392a53bdd5f5396efc0e9cce1a03f09f24bf228ea71e1df8e8c88b71077d9a20 |
|
MD5 | 3884a303c1002527dde440215721d705 |
|
BLAKE2b-256 | b760ddf30d81310aaa158240ff266b947a5b7225f00d89d4cbe4c09845276665 |