phylofunc

'phylofunc' is a Python package for generating phylofunc to incorporate microbiome phylogeny to inform on metaproteomic functional distance. It enables efficient calculation of functional beta-diversity distances between sample pairs and generates comprehensive distance metrics across multiple samples.

Installation of package

You can install this package via pip:
pip install phylofunc

Usage

Once installed, you can use the phylofunc package in a Python script or an interactive environment.

Quick Start

Import package

from phylofunc import PhyloFunc_distance
from phylofunc import PhyloFunc_matrix

Script

Two input parameters are required. The first is a phylogenetic tree (default: bac120_iqtree_v2.0.1.nwk). The second is a phylogeny-informed Taxon-Function table, which includes columns labeled Taxon, Function, and the names of samples (default: Taxon_Function_distance.csvor Taxon_Function_matrix.csv).

1. Calculate phylofunc distance between sample pairs

PhyloFunc_distance(tree_file='bac120_iqtree_v2.0.1.nwk', sample_file='Taxon_Function_distance.csv')

2. Calculate phylofunc distance matrix across multiple samples

PhyloFunc_matrix(tree_file='bac120_iqtree_v2.0.1.nwk', sample_file='Taxon_Function_matrix.csv')

Output

phylofunc distance or phylofunc distance matrix can be output.

Performance optimization

This package improves performance by reducing disk I/O operations and processing data in memory. This enables faster computations with large datasets.

Project structure

phylofunc/  
├── __init__.py  
├── phylofunc.py  
│  └── The main function code.  
├── data/  
│  ├── Taxon_Function_distance.csv
│  │  └── Data file for calculating the distance between two samples. 
│  ├── Taxon_Function_matrix.csv
│  │  └── Data file for calculating distances matrix across multiple samples.  
│  └── bac120_iqtree_v2.0.1.nwk  
│     └── Phylogenetic tree file.  
└── Phylofunc_Package_Tutorial.ipynb
   └── Demonstrates the specific application of this package.

Contribution

Welcome code contributions and improvement suggestions! Feel free to submit an issue or a pull request on GitHub.

License

This project uses an MIT license. For details, see the LICENSE file.

Application

For more detailed usage instructions, please refer to the paper： Wang and Li et al., PhyloFunc: Phylogeny-informed Functional Distance as a New Ecological Metric for Metaproteomic Data Analysis doi: https://doi.org/10.1101/2024.05.28.596184