PUREE v1.0.0 (Python API)

Introduction

PUREE is a compact and fast method for predicting tumor purity (cancer cell fraction) from bulk gene expression data. The methodology and the validation process is described in the paper PUREE: accurate pan-cancer tumor purity estimation from gene expression data. PUREE is also available as a web service at https://puree.genome.sg. If you would like an access to the PUREE's backend code, please contact the corresponding author of the paper.

The PUREE class is a wrapper class that exposes functionality to interact with the PUREE code. The class allows you to monitor the health of the backend, submit a file for processing, and get the logs and the output.

Requirements

This package is tested on Python versions above 3.8. In addition, it has the following dependencies

pandas==1.5.3
requests==2.28.2

Installing and running PUREE

To install PUREE, run the following in the command line:

git clone https://github.com/skandlab/PUREE
cd PUREE
python3 setup.py bdist_wheel
pip install dist/PUREE-0.1.0-py3-none-any.whl --force-reinstall # this can be installed in the environment of your choice

Now you can use PUREE in your Python environment:

from puree import *

p = PUREE()
purities_and_logs = p.get_output(test_data_path, gene_id_nomenclature)

where

variable	description
test_data_path	string; path to the gene expression matrix in .csv or .tsv
gene_id_nomenclature	string; gene ids nomenclature: 'ENSEMBL' or 'HGNC'

Input

PUREE expects a gene expression matrix as input, in any normalization space, preferably oriented with genes as columns and samples as rows. The gene identifiers can be passed as either ENSEMBL IDs or HGNC gene symbols.

More specifically, the expected input would schematically look like this

	gene_id_1	gene_id_2
sample_id_1	10	1
sample_id_2	0	10

Output

PUREE returns a .tsv file with tumor purities in the first column. The output and the logs are stored in a dictionary: {"output": purity_dataframe, "logs": PUREE_logs}.
Note: the sample names will be anonymized. However, the purities are returned in the same order as the samples in the input.