Metadata-Version: 2.1
Name: biotool-ravi
Version: 1.0.0
Summary: A bioinformatics toolkit for DNA sequence analysis, FASTA/GenBank file operations, NCBI queries, sequence alignment, phylogenetics, and protein structure visualization.
Author-email: ravi <ravi424e@gmail.com>
Project-URL: Homepage, https://github.com/ravi424e/biotool-ravi
Project-URL: Repository, https://github.com/ravi424e/biotool-ravi
Project-URL: Bug Tracker, https://github.com/ravi424e/biotool-ravi/issues
Keywords: bioinformatics,dna,sequence-analysis,fasta,genbank,ncbi,alignment,phylogenetics,pdb,biopython
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Education
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython>=1.80
Requires-Dist: matplotlib>=3.5
Requires-Dist: numpy>=1.21

# 🧬 biotool-ravi

A comprehensive Python bioinformatics toolkit for DNA sequence analysis, file format conversion, NCBI queries, sequence alignment, phylogenetics, and protein structure visualization.

## Installation

```bash
pip install biotool-ravi
```

## Features

| Module | Description |
|--------|-------------|
| `seq_operations` | DNA slicing, concatenation, transcription & translation |
| `fasta_reader` | Parse and read FASTA files |
| `genbank_writer` | Create GenBank format files |
| `fasta_to_genbank` | Convert FASTA → GenBank |
| `gene_annotation` | Add annotations and features to sequences |
| `ncbi_fetch` | Fetch sequences from NCBI Entrez |
| `pairwise_align` | Pairwise sequence alignment |
| `muscle_align` | Multiple sequence alignment via MUSCLE |
| `phylo_tree` | Phylogenetic tree construction (UPGMA/NJ) |
| `pdb_viewer` | 3D protein structure visualization |

## Quick Start (Python API)

```python
from biotool import dna_operations, read_fasta, fetch_from_ncbi

# DNA operations
result = dna_operations("ATGCTAGCTAGCTAGCTG", start=3, end=11)
print(result["rna"])       # RNA sequence
print(result["protein"])   # Protein sequence

# Read FASTA file
records = read_fasta("sequences.fasta")

# Fetch from NCBI
data = fetch_from_ncbi("NM_001301717")
print(data["organism"], data["length"])
```

## Command-Line Interface

```bash
# DNA sequence operations
biotool seq-ops --seq ATGCTAGCTAGCTAGCTG

# Read FASTA file
biotool read-fasta sequences.fasta

# Fetch from NCBI
biotool fetch-ncbi NM_001301717

# Pairwise alignment
biotool align-pair --seq1 AGTACACTGGT --seq2 AGTACGCTGGT

# Convert FASTA to GenBank
biotool convert input.fasta output.gb

# Build phylogenetic tree
biotool phylo-tree aligned.fasta --method upgma

# View 3D protein structure
biotool view-pdb 1A3N --save structure.png
```

## Requirements

- Python >= 3.8
- Biopython >= 1.80
- Matplotlib >= 3.5
- NumPy >= 1.21
- MUSCLE (optional, for multiple alignment)

## License

MIT License - see [LICENSE](LICENSE) for details.

## Author

**ravi** — ravi424e@gmail.com
