Metadata-Version: 2.4
Name: ngd
Version: 0.2.0
Summary: A comprehensive bioinformatics package with 10 essential programs
Home-page: https://github.com/yourusername/ngd
Author: Your Name
Author-email: your.email@example.com
Keywords: bioinformatics,dna,rna,protein,sequence,alignment,phylogenetics
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Education
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: biopython>=1.79
Requires-Dist: matplotlib>=3.5.0
Requires-Dist: numpy>=1.21.0
Requires-Dist: pandas>=1.3.0
Requires-Dist: requests>=2.25.0
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: keywords
Dynamic: requires-dist
Dynamic: requires-python
Dynamic: summary

# NGD - Bioinformatics Programs Package

A comprehensive Python package containing 10 essential bioinformatics programs for DNA/RNA analysis, sequence manipulation, and protein structure visualization.

## Installation

You can install the package using pip:

```bash
pip install ngd
```

Or install from source:

```bash
git clone https://github.com/yourusername/ngd.git
cd ngd
pip install -e .
```

## Available Programs

The package includes 10 comprehensive bioinformatics programs:

### 1. **DNA Manipulation and Translation**
- DNA sequence slicing and concatenation
- DNA to RNA transcription
- RNA to protein translation
- Basic sequence operations using Biopython

### 2. **Reading FASTA Files**
- Parse and read FASTA format files
- Extract sequence descriptions and data
- Handle multiple sequences in a single file

### 3. **Writing and Reading GenBank Format**
- Create GenBank records with annotations
- Write sequences to GenBank format
- Read and parse GenBank files
- Handle sequence metadata

### 4. **Converting FASTA to GenBank with Annotations**
- Convert between sequence formats
- Add annotations during conversion
- Batch processing of multiple sequences
- Format validation

### 5. **Adding Features and Annotations to SeqRecord**
- Create detailed sequence records
- Add gene features and annotations
- Modify sequence metadata
- Handle complex biological annotations

### 6. **Fetching Sequences from NCBI using Entrez**
- Access NCBI databases programmatically
- Retrieve GenBank records by ID
- Extract sequence information
- Handle NCBI API responses

### 7. **Pairwise Sequence Alignment**
- Align two DNA sequences
- Calculate alignment scores
- Visualize sequence similarities
- Handle alignment parameters

### 8. **Multiple Sequence Alignment using MUSCLE**
- Perform multiple sequence alignment
- Use external MUSCLE tool
- Handle alignment output
- Process alignment results

### 9. **Constructing Phylogenetic Trees**
- Build phylogenetic trees from alignments
- Calculate distance matrices
- Create UPGMA trees
- Visualize and save tree structures

### 10. **PDB 3D Structure Visualization**
- Download protein structures from PDB
- Parse mmCIF files
- Extract atomic coordinates
- Create 3D structure visualizations

## Usage

To view the code for any program, use the `print_program` function:

```python
from ngd.programs import print_program

# Print program 1 (DNA Manipulation)
print_program(1)

# Print program 2 (FASTA Reading)
print_program(2)

# Print program 3 (GenBank Operations)
print_program(3)

# And so on for programs 4-10...
```

## Requirements

The package requires the following dependencies:
- **biopython** >= 1.79 - Core bioinformatics functionality
- **matplotlib** >= 3.5.0 - Plotting and visualization
- **numpy** >= 1.21.0 - Numerical computations
- **pandas** >= 1.3.0 - Data manipulation
- **requests** >= 2.25.0 - HTTP requests for NCBI access

## Features

- **Comprehensive Coverage**: From basic DNA manipulation to advanced phylogenetic analysis
- **Educational**: Well-commented code suitable for learning bioinformatics
- **Practical**: Real-world applications using popular bioinformatics tools
- **Extensible**: Easy to modify and extend for specific research needs
- **Cross-platform**: Works on Windows, macOS, and Linux

## Examples

### Basic DNA Operations
```python
from ngd.programs import print_program
print_program(1)  # DNA manipulation and translation
```

### Sequence Analysis
```python
from ngd.programs import print_program
print_program(7)  # Pairwise sequence alignment
```

### Database Access
```python
from ngd.programs import print_program
print_program(6)  # NCBI sequence fetching
```

## Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

## License

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

## Citation

If you use this package in your research, please cite:

```
NGD Bioinformatics Package (2024). A comprehensive collection of bioinformatics programs.
Available at: https://pypi.org/project/ngd/
``` 
