Bio.Seq Dependency Guide

Understanding Bio.Seq Import Errors

If you encounter errors like:

ModuleNotFoundError: No module named 'Bio'

or

ImportError: No module named 'Bio.Seq'

Do NOT try to install a package called seq. The solution is to install biopython.

Correct Installation

The Bio.Seq module comes from the biopython package, not a separate "seq" package.

Install biopython:

pip install biopython

Or if using the project requirements:

pip install -r requirements.txt

Understanding the Import

When you see code like:

from Bio.Seq import Seq

This imports the Seq class from the Bio.Seq module, which is part of the biopython library.

Common Confusion

❌ Incorrect: pip install seq (this package doesn't exist) ✅ Correct: pip install biopython

Testing Your Installation

After installing biopython, test that it works:

from Bio.Seq import Seq

# Create a DNA sequence
dna_seq = Seq("ATGCGATCGATC")
print(f"DNA sequence: {dna_seq}")
print(f"Length: {len(dna_seq)}")

Framework Usage with Bio.Seq

The Z Framework's biological sequence analysis modules use Bio.Seq for:

• DNA/RNA sequence handling
• Protein sequence analysis
• Quantum-inspired sequence alignment
• Helical coordinate generation

Example:

from Bio.Seq import Seq
from src.Bio.QuantumTopology import generate_helical_coordinates, quantum_alignment

# Analyze DNA sequences
seq1 = Seq("ATGCGATCGATC")
seq2 = Seq("ATGCGATCGATC")

# Generate helical coordinates using Z Framework
coords = generate_helical_coordinates(seq1)

# Perform quantum-inspired alignment
alignment = quantum_alignment(seq1, seq2)
print(f"Alignment score: {alignment['alignment_score']}")

Troubleshooting

Version Requirements

• Minimum biopython version: 1.83
• Compatible with Python 3.8+

Alternative Installation Methods

# Using conda
conda install -c conda-forge biopython

# Using pip with specific version
pip install biopython>=1.83

Import Error Handling

The framework includes graceful error handling that will show clear messages if biopython is missing:

try:
    from Bio.Seq import Seq
except ImportError:
    print("Bio.Seq requires biopython package. Install with: pip install biopython")

Related Packages

The Z Framework uses these related dependencies for biological analysis:

• biopython: Biological sequence handling (Bio.Seq, Bio.SeqIO)
• numpy: Numerical computations
• scipy: Scientific computing
• matplotlib: Visualization
• plotly: Interactive visualizations (optional)

Support

If you continue to have issues after installing biopython:

1. Check your Python environment
2. Verify biopython version: pip show biopython
3. Test import in a fresh Python session
4. Check for conflicting package installations