# BioinformaticsPipeline Class

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## Overview
The `BioinformaticsPipeline` class provides a collection of static methods for performing common bioinformatics tasks, including sequence alignment, transcription, translation, mutation detection, and simulation of DNA evolution. It also supports analysis of protein-cell interactions.

---

## Class Definition

```python
class BioinformaticsPipeline:
    @staticmethod
    def align_sequences(seq1: str, seq2: str) -> Tuple[str, str]:
        """
        Perform a simple global sequence alignment using the Needleman-Wunsch algorithm.
        :param seq1: First sequence to align
        :param seq2: Second sequence to align
        :return: Tuple of aligned sequences
        """
        ...
```

---

## Methods

### Sequence Alignment
- **`align_sequences(seq1: str, seq2: str) -> Tuple[str, str]`**
  Performs a global sequence alignment using the Needleman-Wunsch algorithm.

  - **Parameters**:
    - `seq1`: First sequence to align.
    - `seq2`: Second sequence to align.

  - **Returns**: A tuple of aligned sequences.

  - **Details**:
    - Uses a scoring matrix to align sequences with matches, mismatches, and gaps.
    - Implements traceback to construct the aligned sequences.

---

### Transcription
- **`transcribe_dna(dna_sequence: str) -> str`**
  Transcribes a DNA sequence to RNA.

  - **Parameters**:
    - `dna_sequence`: DNA sequence to transcribe.

  - **Returns**: Transcribed RNA sequence.

  - **Details**:
    - Replaces thymine (T) with uracil (U).

---

### Translation
- **`translate_rna(rna_sequence: str) -> str`**
  Translates an RNA sequence to a protein sequence.

  - **Parameters**:
    - `rna_sequence`: RNA sequence to translate.

  - **Returns**: Protein sequence.

  - **Details**:
    - Uses a codon table to translate RNA codons to amino acids.
    - Stops translation at stop codons.

---

### Mutation Detection
- **`find_mutations(seq1: str, seq2: str) -> List[Tuple[int, str, str]]`**
  Finds mutations between two aligned sequences.

  - **Parameters**:
    - `seq1`: First sequence.
    - `seq2`: Second sequence.

  - **Returns**: A list of tuples, each containing the position, nucleotide in `seq1`, and nucleotide in `seq2`.

---

### Evolution Simulation
- **`simulate_evolution(dna: DNA, generations: int, mutation_rate: float) -> DNA`**
  Simulates the evolution of a DNA sequence over multiple generations.

  - **Parameters**:
    - `dna`: Initial DNA object.
    - `generations`: Number of generations to simulate.
    - `mutation_rate`: Probability of mutation per nucleotide.

  - **Returns**: Evolved DNA object.

  - **Details**:
    - Simulates replication and mutation over multiple generations.

---

### Protein-Cell Interaction Analysis
- **`analyze_protein_interactions(protein: Protein, cell: Cell) -> str`**
  Analyzes interactions between a protein and a cell.

  - **Parameters**:
    - `protein`: Protein object.
    - `cell`: Cell object.

  - **Returns**: A string describing the interactions.

  - **Details**:
    - Checks for receptor bindings and surface protein interactions.
    - Analyzes protein activity.

---

## Example Usage

```python
# Align sequences
seq1 = "ATGCGATCG"
seq2 = "ATGCCATG"
aligned_seq1, aligned_seq2 = BioinformaticsPipeline.align_sequences(seq1, seq2)
print(f"Aligned sequence 1: {aligned_seq1}")
print(f"Aligned sequence 2: {aligned_seq2}")

# Transcribe DNA to RNA
dna_sequence = "ATGCGATCG"
rna_sequence = BioinformaticsPipeline.transcribe_dna(dna_sequence)
print(f"RNA sequence: {rna_sequence}")

# Translate RNA to protein
protein_sequence = BioinformaticsPipeline.translate_rna(rna_sequence)
print(f"Protein sequence: {protein_sequence}")

# Find mutations
mutations = BioinformaticsPipeline.find_mutations(seq1, seq2)
print(f"Mutations: {mutations}")

# Simulate DNA evolution
dna = DNA(sequence="ATGCGATCGATCGATCGATCGATCGATCGATCG")
evolved_dna = BioinformaticsPipeline.simulate_evolution(dna, generations=5, mutation_rate=0.01)
print(f"Evolved DNA sequence: {evolved_dna.sequence}")

# Analyze protein-cell interactions
protein = Protein("Example Protein", " ")
cell = Cell("Example Cell", "Liver")
interaction_result = BioinformaticsPipeline.analyze_protein_interactions(protein, cell)
print(interaction_result)
```

---

## Dependencies
- **`biobridge.genes.dna.DNA`**: For DNA objects.
- **`biobridge.blocks.protein.Protein`**: For protein objects.
- **`biobridge.blocks.cell.Cell`**: For cell objects.

---

## Error Handling
- The class does not explicitly handle errors, but it relies on the underlying methods of the DNA, protein, and cell classes to handle their own errors.

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## Notes
- The `BioinformaticsPipeline` class is designed to perform common bioinformatics tasks.
- It supports sequence alignment, transcription, translation, mutation detection, and simulation of DNA evolution.
- The class also supports analysis of protein-cell interactions.
- All methods are static, allowing for easy integration and usage without instantiation.
