# DNASequencer Class

---

## Overview
The `DNASequencer` class simulates the process of DNA sequencing, including the introduction of sequencing errors and the assembly of sequenced reads into a complete DNA sequence. It also provides methods for analyzing the quality of the sequencing process.

---

## Class Definition

```python
class DNASequencer:
    def __init__(self, error_rate: float = 0.001, read_length: int = 100):
        """
        Initialize a DNA Sequencer.
        :param error_rate: Probability of a sequencing error (default: 0.001)
        :param read_length: Length of each read (default: 100 nucleotides)
        """
        ...
```

---

## Attributes

| Attribute | Type | Description |
|-----------|------|-------------|
| `error_rate` | `float` | Probability of a sequencing error. |
| `read_length` | `int` | Length of each read in nucleotides. |

---

## Methods

### Initialization
- **`__init__(self, error_rate: float = 0.001, read_length: int = 100)`**
  Initializes a new `DNASequencer` instance with the specified error rate and read length.

---

### DNA Sequencing
- **`sequence(self, dna: str) -> List[str]`**
  Sequences the given DNA, simulating the physical process with potential errors.

  - **Parameters**:
    - `dna`: The DNA sequence to be sequenced.

  - **Returns**: List of sequenced reads.

  - **Details**:
    - The DNA is divided into reads of the specified length.
    - Each read may contain sequencing errors.

---

### Error Introduction
- **`_introduce_errors(self, read: str) -> str`**
  Introduces sequencing errors into a read.

  - **Parameters**:
    - `read`: The original read.

  - **Returns**: The read with potential errors.

  - **Details**:
    - Errors can be substitutions, insertions, or deletions.
    - The type and position of errors are determined randomly based on the error rate.

---

### Sequence Assembly
- **`assemble(self, reads: List[str]) -> str`**
  Assembles the sequenced reads into a complete DNA sequence.

  - **Parameters**:
    - `reads`: List of sequenced reads.

  - **Returns**: Assembled DNA sequence.

  - **Details**:
    - The assembly process starts with the longest read.
    - Subsequent reads are added based on overlaps with the assembled sequence.

---

### Overlap Detection
- **`_find_overlap(self, seq1: str, seq2: str) -> int`**
  Finds the overlap between two sequences.

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

  - **Returns**: Length of the overlap.

---

### Quality Analysis
- **`analyze_quality(self, original: str, sequenced: str) -> Tuple[float, float, float]`**
  Analyzes the quality of the sequencing by comparing the original and sequenced DNA.

  - **Parameters**:
    - `original`: The original DNA sequence.
    - `sequenced`: The sequenced DNA.

  - **Returns**: Tuple of (accuracy, coverage, average_read_length).

  - **Details**:
    - **Accuracy**: Proportion of matching nucleotides between the original and sequenced DNA.
    - **Coverage**: Ratio of the length of the sequenced DNA to the original DNA.
    - **Average Read Length**: Average length of the sequenced reads.

---

## Example Usage

```python
# Initialize a DNA sequencer
sequencer = DNASequencer(error_rate=0.001, read_length=100)

# Define a DNA sequence
dna_sequence = "ATGCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG"

# Sequence the DNA
reads = sequencer.sequence(dna_sequence)
print(f"Sequenced reads: {reads}")

# Assemble the reads
assembled_sequence = sequencer.assemble(reads)
print(f"Assembled sequence: {assembled_sequence}")

# Analyze the quality of the sequencing
accuracy, coverage, avg_read_length = sequencer.analyze_quality(dna_sequence, assembled_sequence)
print(f"Accuracy: {accuracy:.2%}")
print(f"Coverage: {coverage:.2f}")
print(f"Average read length: {avg_read_length:.2f}")
```

---

## Dependencies
- **`random`**: For simulating random sequencing errors.

---

## Error Handling
- The class does not explicitly handle errors, but it includes checks to avoid index errors when processing sequences.

---

## Notes
- The `DNASequencer` class is designed to simulate the DNA sequencing process.
- It supports the introduction of sequencing errors, including substitutions, insertions, and deletions.
- The class provides a simplified assembly process for reconstructing the original sequence from reads.
- The `analyze_quality` method allows for evaluating the accuracy, coverage, and read length of the sequencing process.
