https://github.com/engkinandatama/ncbi-sequence-fetcher
NCBI Sequence Fetcher is a Python desktop app for downloading nucleotide sequences and extracting metadata from NCBI. It features an easy-to-use GUI, supports FASTA and GenBank formats, and helps researchers students and bioinformaticians efficiently collect DNA sequences and store metadata in Excel files.
https://github.com/engkinandatama/ncbi-sequence-fetcher
academic bioinformatics bioinformatics-tool data-scraping fasta genbank metadata metadata-extraction molecular-biology ncbi nucleotide-sequences python tkinter
Last synced: about 1 month ago
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NCBI Sequence Fetcher is a Python desktop app for downloading nucleotide sequences and extracting metadata from NCBI. It features an easy-to-use GUI, supports FASTA and GenBank formats, and helps researchers students and bioinformaticians efficiently collect DNA sequences and store metadata in Excel files.
- Host: GitHub
- URL: https://github.com/engkinandatama/ncbi-sequence-fetcher
- Owner: engkinandatama
- License: mit
- Created: 2025-05-12T20:21:40.000Z (about 1 month ago)
- Default Branch: main
- Last Pushed: 2025-05-12T21:03:42.000Z (about 1 month ago)
- Last Synced: 2025-05-12T21:42:36.818Z (about 1 month ago)
- Topics: academic, bioinformatics, bioinformatics-tool, data-scraping, fasta, genbank, metadata, metadata-extraction, molecular-biology, ncbi, nucleotide-sequences, python, tkinter
- Language: Python
- Homepage:
- Size: 13.7 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 🧬 NCBI Sequence Fetcher
A lightweight and user-friendly desktop application for downloading nucleotide sequences and extracting biological metadata directly from NCBI.
Built with Python and Tkinter, designed for researchers, students, and bioinformaticians.
---
### ⚠️ **Note**:
> **This repository is for personal and educational use only.**
> It is not currently open for external collaboration or contribution.
> Please use responsibly and cite NCBI appropriately when using downloaded data.
---
## 📸 GUI Preview
Coming soon — stay tuned!
---
## ✨ Features
- 🔗 **Direct URL Input**: Download GenBank/FASTA files from any valid NCBI nuccore link.
- 📁 **FASTA / GenBank Format Support**: Choose your preferred sequence format.
- 🧬 **Automatic Metadata Extraction**:
- Accession, Organism, Strain, Taxonomy, Country, Collection Date, Length, etc.
- 📄 **Excel Export**:
- All metadata saved in a clean Excel file (`ncbi_metadata.xlsx`)
- 🏷️ **Smart File Naming**:
- Files saved with informative names: `Organism_Strain_Accession_Length_Feature.fasta`
- 🖥️ **GUI Based**:
- No command line needed; simple Tkinter-based interface.
---
## 🛠️ Technologies Used
- **Language**: Python 3.8+
- **Libraries**:
- `requests`
- `pandas`
- `openpyxl`
- `tkinter` (built-in)
---
## 🚀 Installation & Usage
### 🔧 Step 1: Clone the repository
```bash
git clone https://github.com/engkinandatama/NCBI-Sequence-Fetcher.git
```
```
cd ncbi-data-scraper
```
### 📦 Step 2: Install dependencies
```
pip install -r requirements.txt
```
### ▶️ Step 3: Run the app
```
python ncbi_scraper.py
```
---
## 🧪 How It Works
1. **Paste a valid NCBI URL**
Example: https://www.ncbi.nlm.nih.gov/nuccore/JN188370.1
2. **Choose the format**
`fasta` or `genbank`
3. **Select a destination folder**
Where the sequence file and Excel metadata will be saved
4. **Click `Download`**
---
### 🔄 Behind the Scenes:
The app will:
- 🔍 **Fetch** the nucleotide data directly from NCBI
- 💾 **Save** the sequence locally as: `.fasta` if FASTA format is selected, `.gb` (GenBank) if GenBank format is selected
- 🧬 **Parse and extract metadata**: Accession, Organism, Strain, Country, Date, and more
- 📊 **Append** the metadata into an Excel file: `ncbi_metadata.xlsx`
---
## 📁 Output Example
Setelah proses selesai, file output akan tersimpan seperti berikut:
```
📂 Output_Folder/
├── Escherichia_coli_K12_JN188370.1_4500bp_partial_cds.fasta
└── ncbi_metadata.xlsx
```
- **FASTA / GenBank File**: Berisi urutan nukleotida yang diunduh dari NCBI.
- **ncbi_metadata.xlsx**: File Excel yang berisi metadata terstruktur dari setiap entri GenBank yang diunduh.
---
## 📜 License
This project is licensed under the **MIT License**.
> **Disclaimer**:
> This tool is developed solely for **academic and personal research purposes**.
> Commercial use, bulk data scraping, or redistribution of NCBI content may **violate NCBI's usage policies** and is **strongly discouraged**.
>
> The developer **does not take any responsibility** for misuse, legal issues, or policy violations resulting from the use of this tool.
> **Users are fully responsible** for ensuring their usage complies with relevant terms, laws, and guidelines.
>
> See [NCBI's policies](https://www.ncbi.nlm.nih.gov/home/about/policies/) for more information.