mutcleaner 0.6.0

An efficient framework for cleaning, standardizing, and processing biological mutation data.

MutCleaner

MutCleaner is an extensible Python toolkit for cleaning and standardizing biological mutation datasets, integrating dataset-specific cleaning pipelines with core abstractions for protein, nucleotide, and codon-level mutation representations.

• Documentation: https://xulab-research.github.io/MutCleaner
• Cleaning Examples: https://xulab-research.github.io/MutCleaner/user_guide/supported_datasets.html

Overview

MutCleaner is an extensible Python toolkit for cleaning, standardizing, and analyzing biological mutation datasets. It currently focuses on protein variant data while providing core abstractions for DNA, RNA, protein sequences, and codon-level mutation representations.

The package combines dataset-specific cleaning pipelines with reusable sequence and mutation utilities, enabling reproducible preprocessing of large-scale mutational datasets for downstream bioinformatics and machine learning analyses.

Key Capabilities

• Mutation dataset cleaning and standardization: Harmonize mutation annotations, sequences, labels, and metadata across heterogeneous biological mutation datasets.
• Sequence representation and validation: Utilities for DNA, RNA, and protein sequences, including validation, transcription, reverse transcription, translation, and mutation application.
• Mutation parsing and transformation: Tools for parsing amino-acid and codon-level mutations, inferring mutations from sequences, applying mutations to reference sequences, and converting codon mutations into amino-acid changes.
• Modular pipeline architecture: A composable pipeline interface for building reproducible dataset-cleaning workflows.
• Parallel and scalable dataset processing: Multi-core utilities for mutation validation, mutation application, and sequence-based mutation inference, supporting efficient processing of large tabular mutation datasets.

Installation

Requirements

• Python 3.13+
• Dependencies are automatically installed via pip.

Install via pip

pip install mutcleaner

Development Installation

git clone https://github.com/xulab-research/MutCleaner.git MutCleaner
cd MutCleaner
pip install -e .

To install development dependencies for testing and documentation:

pip install -e ".[dev]"

Package Structure

mutcleaner/
├── cleaners/                # Reusable cleaners and dataset-specific pipelines
│   ├── basic_cleaners.py    # Reusable basic cleaning functions
│   ├── base_config.py       # Shared cleaner configuration
│   └── *_cleaner.py         # Dataset-specific cleaning pipelines
├── core/                    # Core data structures and processing logic
│   ├── alphabet.py          # Biological alphabet definitions and validation
│   ├── codon.py             # Codon table and sequence translation utilities
│   ├── constants.py         # Shared biological constants
│   ├── dataset.py           # Standard dataset abstraction and export logic
│   ├── mutation.py          # Mutation parsing, representation and validation
│   ├── pipeline.py          # Reusable data cleaning pipeline framework
│   ├── sequence.py          # DNA, RNA and protein sequence abstractions
│   └── types.py             # Shared type aliases and annotations
└── utils/                   # General helper functions for downloading and I/O

Module Overview

mutcleaner.cleaners

The cleaners module provides both reusable cleaning functions and predefined dataset-specific cleaning pipelines.

basic_cleaners.py contains general-purpose cleaning functions that can be reused across different datasets, such as column checking, missing value handling, sequence validation, mutation validation, and common formatting operations.
base_config.py defines shared configuration used by dataset cleaners, such as common column names, required fields, and reusable cleaner settings.
*_cleaner.py files define dataset-specific cleaning pipelines. Each file is designed for a particular dataset or benchmark and combines reusable cleaning functions into a complete workflow.

mutcleaner.core

The core module contains the fundamental data structures and processing logic used throughout MutCleaner.

alphabet.py defines biological alphabets and validation rules for DNA, RNA, and protein sequences.
codon.py provides codon table utilities and sequence translation functionality. constants.py stores shared biological constants, such as amino acid symbols, nucleotide symbols, complements, and stop codon definitions.
dataset.py defines the standard dataset abstraction used to store, manage, validate, and export cleaned mutation datasets.
mutation.py provides mutation parsing, mutation representation, and mutation validation logic.
pipeline.py defines the reusable data cleaning pipeline framework, including pipeline steps, execution order, and artifact tracking.
sequence.py defines biological sequence abstractions, including DNA, RNA, and protein sequence classes.
types.py stores shared type aliases and annotations used across the package.

mutcleaner.utils

The utils module contains helper functions that support common operations outside the core cleaning logic.
It includes utilities for downloading source files, handling paths, extracting files, checking file existence, and managing common input/output operations.

Quick Start

See the Data Cleaners Usage Guide for more examples.

Supported Datasets

Dataset Name	Reference	File
Human Domainome Dataset	Site-saturation mutagenesis of 500 human protein domains	SupplementaryTable4.txtSupplementaryTable2.txt, wild_type.fasta
ProteinGym DMS Substitutions Dataset	ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction	DMS_ProteinGym_substitutions.zip
cDNA Proteolysis Dataset	Mega-scale experimental analysis of protein folding stability in biology and design	Tsuboyama2023_Dataset2_Dataset3_20230416.csv
ddG Dataset	Improving the prediction of protein stability changes upon mutations by geometric learning and a pre-training strategy	M1261.csv, S461.csv, S669.csv, S783.csv, S8754.csv
dTm Dataset	Improving the prediction of protein stability changes upon mutations by geometric learning and a pre-training strategy	S4346.csv, S557.csv
ArchStabMS1E10 Epistasis Dataset	The genetic architecture of protein stability	ArchStabMS1E10_Epistasis_Dataset.csv
Antitoxin ParD3 Epistasis Dataset	Protein design using structure-based residue preferences	Antitoxin_ParD3_Epistasis_Dataset.csv
TrpB Epistasis Dataset	A combinatorially complete epistatic fitness landscape in an enzyme active site	TrpB_Epistasis_Dataset.csv
Human Myoglobin Epistasis Dataset	Decoding Stability and Epistasis in Human Myoglobin by Deep Mutational Scanning and Codon-level Machine Learning	Human_Myoglobin_Epistasis_Dataset.csv
CTXM Epistasis Dataset	Network of epistatic interactions in an enzyme active site revealed by DMS	CTXM_Cefotaxime_Epistasis_Dataset.csv, CTXM_Ampicillin_Epistasis_Dataset.csv
RBD ACE2 Dataset	Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution	SARS-CoV-2-RBD_DMS_variants_bc_binding.csv SARS-CoV-2-RBD_Delta_bc_binding.csv
	Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains	SARS-CoV-2-RBD_DMS_Omicron_bc_binding.csv
	Deep mutational scans of XBB.1.5 and BQ.1.1 reveal ongoing epistatic drift during SARS-CoV-2 evolution	SARS-CoV-2-RBD_DMS_Omicron-XBB-BQ_bc_binding.csv
	Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant	SARS-CoV-2-RBD_DMS_Omicron-EG5-FLip-BA286_bc_binding.csv
RBD Antibody Dataset	The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD	SARS-CoV-2-RBD_MAP_Moderna.csv
	Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies	SARS-CoV-2-RBD_MAP_Rockefeller.csv
	SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape	SARS-CoV-2-RBD_MAP_Vir_mAbs.csv
Chitosanase dTm Dataset	In-house wet-lab data, no reference available yet	Chitosanase_dTm_Dataset.csv
MGnify ddG Dataset	Accurate protein stability prediction for small domains using mega-scale experiments	MGnify_ddG_Dataset.csv

Core Features

Sequence Data Manipulation

• Sequence validation: Validate DNA, RNA, and protein sequences against predefined alphabets.
• Sequence transformation: Support transcription, reverse transcription, translation, and reverse-complement operations.
• Batch processing: Process large tabular mutation datasets through reusable cleaning utilities.

Mutation Analysis

• Mutation parsing: Parse amino-acid and codon-level mutation annotations.
• Mutation inference: Infer mutation annotations by comparing reference and mutated sequences.
• Mutation transformation: Apply mutation annotations to reference sequences and convert codon-level mutations into amino-acid changes.

Data Cleaning and Preprocessing

• Standardization: Harmonize mutation names, sequences, labels, and metadata across heterogeneous datasets.
• Duplicate handling: Remove or aggregate redundant mutation records according to dataset-specific rules.
• Dataset-specific cleaners: Provide reusable cleaning pipelines for commonly used mutation datasets.

Pipeline Architecture

• Modular design: Compose cleaning workflows from reusable processing components.
• Parallel processing: Use multi-core processing for mutation validation, mutation application, and sequence-based mutation inference.
• Progress tracking: Monitor long-running cleaning tasks with progress bars and structured execution summaries.

Citation

If you use MutCleaner in your research, please cite:

@software{mutcleaner,
  title={
    MutCleaner: An efficient framework for cleaning, standardizing, and processing biological mutation data.
  },
  author={Ziyu Shi and Yuxiang Tang},
  year={2026},
  url={https://github.com/xulab-research/MutCleaner}
}

License

This project is licensed under the Apache License 2.0.

Unless otherwise stated, the source code, model architecture, training scripts, inference scripts, and released model weights/checkpoints are licensed under Apache-2.0.

Datasets used in this project may be subject to their original licenses and terms of use. Please refer to the corresponding dataset sources for details.

This software is provided for research purposes and is not intended for clinical diagnosis, medical decision-making, or direct therapeutic use.