biobase 0.5.1

A comprehensive package of biological constants, serving as a foundational resource for biology and bioinformatics, complemented by functions to streamline related tasks.

Biobase

A Python package providing standardized biological constants and scoring matrices for bioinformatics pipelines. Biobase aims to eliminate the need to repeatedly recreate common biological data structures and scoring systems in your code.

Table of Contents

• Quick Start
  • Access amino acid properties
  • Use scoring matrices
  • Analyze DNA sequences
  • Find protein motifs
  • Parse FASTA
• Requirements
• Installation
  • Regular Installation
  • Development Installation
• Running Files
• Data Files
• Project Goals
• Contributing
• Project Status
• License

Quick Start

Access amino acid properties

from biobase.constants import ONE_LETTER_CODES, MONO_MASS
print(ONE_LETTER_CODES)  # 'ACDEFGHIKLMNPQRSTVWY'
print(MONO_MASS['A'])    # 71.037113805
`FastaRecord``

Use scoring matrices

from biobase.matrix import Blosum
blosum62 = Blosum(62)
print(blosum62['A']['A'])  # 4
print(blosum62['W']['C'])  # -2

Analyze DNA sequences

from biobase.analysis import Dna
sequence = "ATCGTAGC"
print(Dna.transcribe(sequence))         # 'AUCGUAGC'
print(Dna.complement_dna(sequence))     # 'GCTACGAT'
print(Dna.calculate_gc_content(sequence))  # 50.0

Find protein motifs

from biobase.analysis import find_motifs
sequence = "ACDEFGHIKLMNPQRSTVWY"
print(find_motifs(sequence, "DEF"))  # [3]

Parse FASTA

from biobase.parser import fasta_parser
records = fasta_parser(fasta)
for r in records:
    print(r.id) # CAA39742.1
    print(r.seq) # MTNIRKSHPLMKII...

Requirements

• Python 3.10+
• pip (for installation)

Installation

Regular Installation

pip install biobase

Development Installation

Clone the repository and install in editable mode:

git clone https://github.com/lignum-vitae/biobase.git
cd biobase
pip install -e .

Running Files

To ensure relative imports work correctly, always run files using the module path from the project root:

Run a specific file

python -m src.biobase.matrix

Data Files

• src/biobase/matrices/: Scoring matrix data stored in JSON file format

Project Goals

Biobase aims to provide Python-friendly versions of common biological constants and tools for bioinformatics pipelines. Key objectives:

1. Standardize biological data structures
2. Provide efficient implementations of common scoring systems
3. Ensure type safety and validation
4. Maintain comprehensive documentation
5. Support modern Python practices

Contributing

We welcome contributions! Please read our:

• Code of Conduct
• Contribution Guidelines

Project Status

Current Version: 0.4.1-alpha

Core Features

• ✅ BLOSUM and PAM matrix implementations
• ✅ Basic amino acid constants and conversions
• ✅ DNA/RNA sequence analysis tools
• ✅ Protein motif searching
• ✅ Core biological constants
• ✅ Additional scoring matrices
• ✅ Extended amino acid properties

Analysis Tools

• ✅ GC content calculation
• ✅ DNA/RNA transcription
• ✅ DNA complementation
• ✅ Motif finding
• 🚧 File format parsers (FASTA, GenBank, etc.)
• 📋 Statistical analysis tools

Documentation

• ✅ Basic README
• ✅ Code of Conduct
• ✅ Contributing Guidelines
• ✅ Usage Examples

Development

• ✅ PyPI package deployment
• 🚧 CI/CD Pipeline
• 🚧 Code Coverage
• 📋 Automated Releases

Legend

• ✅ Complete
• 🚧 In Progress
• 📋 Planned

Stability

This project is in the alpha stage. APIs may change without warning until version 1.0.0.

License

This project is licensed under the MIT License - see the LICENSE file for details.