Metadata-Version: 2.4
Name: bioutils-collection
Version: 0.2.0
Summary: Comprehensive bioinformatics utilities for sequence analysis, alignment, annotation, and molecular biology workflows
Author: MForofontov
License: MIT License
        
        Copyright (c) 2026 Mykyta Forofontov
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
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        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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Project-URL: Homepage, https://github.com/MForofontov/bioutils-collection
Project-URL: Repository, https://github.com/MForofontov/bioutils-collection
Project-URL: Issues, https://github.com/MForofontov/bioutils-collection/issues
Project-URL: Documentation, https://github.com/MForofontov/bioutils-collection#readme
Keywords: bioinformatics,genomics,sequence-analysis,alignment,fasta,dna,rna,protein,annotation,molecular-biology
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Typing :: Typed
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=2.3.0
Requires-Dist: scipy>=1.15.0
Requires-Dist: scikit-learn>=1.7.0
Requires-Dist: numba>=0.60.0
Provides-Extra: dev
Requires-Dist: pytest==8.4.1; extra == "dev"
Requires-Dist: pytest-asyncio==1.1.0; extra == "dev"
Requires-Dist: pytest-cov==7.0.0; extra == "dev"
Requires-Dist: mypy==1.17.1; extra == "dev"
Requires-Dist: ruff; extra == "dev"
Requires-Dist: attrs==25.3.0; extra == "dev"
Dynamic: license-file

# 🧬 Bioutils Collection

[![PyPI version](https://badge.fury.io/py/bioutils-collection.svg)](https://pypi.org/project/bioutils-collection/)
[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

> **Production-ready bioinformatics toolkit** - 77+ optimized functions for sequence analysis, alignment, annotation, and molecular biology workflows.

## ✨ Highlights

- 🚀 **77+ specialized functions** across 13 bioinformatics domains
- 🔒 **Fully typed** with complete type hints (mypy strict)
- 📊 **Research-grade algorithms** - Needleman-Wunsch, Smith-Waterman, and more
- ⚡ **Performance optimized** for large-scale genomic data
- ✅ **Extensively tested** with comprehensive test coverage
- 📝 **Self-documenting** - NumPy-style docstrings with examples

## 📦 Installation

```bash
pip install bioutils-collection
```

**Requirements:** Python 3.10+ with numpy, scipy, and scikit-learn

## 🎯 Quick Start

```python
from bioutils_collection import (
    reverse_complement,
    gc_content,
    needleman_wunsch,
    parse_fasta,
    translate_dna_to_protein,
)

# Sequence manipulation
seq = "ATCGATCG"
rev_comp = reverse_complement(seq)  # "CGATCGAT"

# Calculate GC content
gc = gc_content("ATCGATCG")  # 0.5

# Global sequence alignment
seq1, seq2 = "GATTACA", "GCATGCU"
aligned1, aligned2, score = needleman_wunsch(seq1, seq2)

# Parse FASTA files
for header, sequence in parse_fasta("genome.fasta"):
    print(f"{header}: {len(sequence)} bp")

# Translate DNA to protein
protein = translate_dna_to_protein("ATGGCCTAA")  # "MA*"
```

## 🧬 Modules

### Core Sequence Operations
- **`alignment_functions`** - Pairwise & multiple sequence alignment (Needleman-Wunsch, Smith-Waterman, BLAST score ratio)
- **`sequence_operations`** - Reverse complement, ORF finding, CpG islands, low-complexity filtering
- **`translation_functions`** - DNA↔RNA transcription, translation with custom codon tables

### Sequence Analysis & Statistics
- **`gc_functions`** - GC content, GC skew, windowed GC profiling
- **`sequence_statistics`** - Codon usage (CAI, ENC, RSCU), melting temp, isoelectric point, amino acid composition
- **`data_validation`** - DNA/RNA/protein sequence validation

### File I/O & Parsing
- **`fasta_misc`** - FASTA parsing, writing, filtering, splitting, concatenation, primer generation
- **`annotation_functions`** - BED/GFF/GTF/VCF parsing and conversion, annotation statistics

### Pattern & Motif Discovery
- **`motif_functions`** - Motif search, consensus generation, pattern matching
- **`repeat_functions`** - Tandem repeat finder, palindrome detection
- **`restriction_functions`** - Restriction enzyme site identification
- **`clustering_functions`** - Motif clustering and grouping

## 🔬 Use Cases

**Genomic Analysis**
```python
from bioutils_collection import find_orfs, gc_content_windows, find_cpg_islands

# Find all ORFs in a sequence
orfs = find_orfs(dna_sequence, min_length=300)

# Sliding window GC analysis
gc_proDevelopment

```bash
# Clone repository
git clone https://github.com/MForofontov/bioutils-collection.git
cd bioutils-collection

# Install with dev dependencies
pip install -e ".[dev]"

# Run tests
pytest

# Run specific test categories
pytest -m alignment
pytest -m fasta
pytest -m translation

# Type checking
mypy bioutils_collection

# Linting
ruff check .

# Coverage report
pytest --cov=bioutils_collection --cov-report=html
```

## 📚 API Documentation

All functions include:
- ✅ **Complete type hints** for static analysis
- 📖 **NumPy-style docstrings** with parameter descriptions
- 💡 **Usage examples** in docstrings
- ⚠️ **Complexity notes** for performance-critical code
- 📎 **Algorithm references** where applicable

Example:
```python
from bioutils_collection import needleman_wunsch
help(needleman_wunsch)  # Comprehensive documentation
```

## 🤝 Contributing

Contributions welcome! Please:

1. Fork the repository
2. Create a feature branch (`git checkout -b feature/amazing-feature`)
3. Add comprehensive tests
4. Ensure all tests pass (`pytest`)
5. Add type hints and docstrings
6. Submit a pull request

**Development Guidelines:**
- Follow existing code style (ruff formatting)
- Add tests for all new functions
- Update documentation
- Keep functions focused and single-purpose

## 🔗 Related Projects

- **[BioPython](https://biopython.org/)** - Comprehensive biological computation library
- **[scikit-bio](http://scikit-bio.org/)** - Scientific Python library for bioinformatics
- **[pyutils-collection](https://github.com/MForofontov/pyutils-collection)** - General Python utilities (sister project)

# Protein properties
pi = calculate_isoelectric_point(protein_seq)
composition = amino_acid_composition(protein_seq)

# Primer design
tm = melting_temperature("ATCGATCGATCG")
```

## 🧪 Testing

```bash
# Run all tests
pytest

# Run specific module tests
pytest -m alignment
pytest -m fasta
pytest -m translation

# Run with coverage
pytest --cov=bioutils_collection --cov-report=html
```

## 📖 Documentation

Each function includes:
- **� License

MIT License - see [LICENSE](LICENSE) for details.

## 📊 Project Stats

- **77+ Functions** across 13 specialized modules
- **670+ Tests** with comprehensive coverage
- **Type-safe** with mypy strict mode
- **Python 3.10+** with modern type hints

## 📮 Contact & Support

- **Author:** Mykyta Forofontov
- **Repository:** [github.com/MForofontov/bioutils-collection](https://github.com/MForofontov/bioutils-collection)
- **Issues:** [Report bugs or request features](https://github.com/MForofontov/bioutils-collection/issues)
- **PyPI:** [pypi.org/project/bioutils-collection](https://pypi.org/project/bioutils-collection/)

---

Star this repo if you find it useful!

## Contributing

Contributions are welcome! Please:
1. Fork the repository
2. Create a feature branch
3. Add tests for new functionality
4. Ensure all tests pass
5. Submit a pull request

## 📄 License

MIT License - see [LICENSE](LICENSE) file for details.

## 🔗 Related Projects

- [BioPython](https://biopython.org/) - Comprehensive bioinformatics toolkit
- [scikit-bio](http://scikit-bio.org/) - Scientific Python library for bioinformatics

## 📮 Contact

**Author:** Mykyta Forofontov  
**Repository:** https://github.com/MForofontov/bioutils-collection  
**Issues:** https://github.com/MForofontov/bioutils-collection/issues
