immunoraptor 0.0.1
ImmunoRAPTOR predicts proteasomal cleavage and peptide production preference between standard and immunoproteasome.
Requires Python: >=3.11

# **ImmunoRAPTOR**

ImmunoRAPTOR is a computational tool designed to predict proteasomal cleavage and peptide production preferences, comparing the **immunoproteasome (IP)** to the **standard proteasome (SP)**.

This repository contains immunoRAPTOR Python library with API and simple web-based graphical user interface (GUI).

## **Installation**

### Step 1: Install Python

1. Go to [python.org/downloads](https://www.python.org/downloads/)
2. Download Python 3.11 or newer
3. **Important**: During installation, check the box "Add Python to PATH"
4. Click "Install Now"

### Step 2: Open Terminal/Command Prompt

- **Windows**: 
  - Press `Windows key + R`
  - Type `cmd` and press Enter
  
- **Mac**: 
  - Press `Command + Space`
  - Type `Terminal` and press Enter
  
- **Linux**: 
  - Press `Ctrl + Alt + T`

### Step 3: Install ImmunoRAPTOR

Copy and paste this command into terminal, then press Enter:
```bash
pip install immunoraptor
```

Wait for the installation to complete (may take 1-2 minutes).

## **Usage**

Copy and paste this command into terminal, then press Enter:
```bash
immunoraptor-gui
```

Your web browser will automatically open with the interface at `http://localhost:5000`. If not, open your web browser and visit `http://localhost:5000`.

### Example of using the API
```python
from immunoraptor import peptide_ip_vs_sp

result = peptide_ip_vs_sp('STQR', 'MLIKRTMQS', 'ILRT')
print(f'peptide IP vs SP: {result}')
```

## **Analysis Modes (GUI)**

The web interface provides four distinct analysis modes:

### **1\. Cleavage IP vs SP**

* **What it computes:** Predicts the cleavage preference (IP vs. SP) for one or more given cleavage windows.  
* **Inputs:**  
  * **Cleavage Windows:** A list of amino acid sequences, with one window per line.  
  * You can also upload a .txt or .csv file containing the list.  
* **Outputs:**  
  * A results table with two columns: **Cleavage Window** and **Score**.  
  * A button to download the results as a .csv file.

### **2\. Peptide IP vs SP**

* **What it computes:** Predicts the peptide production preference (IP vs. SP) for peptides based on their sequence and their N- and C-terminal extensions.  
* **Inputs:**  
  * **Comma-separated input:** A list of peptides in the format N-term,peptide,C-term (e.g., NTRM,PEPTIDE,CTRM). Each entry must be on a new line.  
  * **File Upload:** You can also upload a .txt or .csv file with the same format.  
  * **Peptide production mode:** A choice between "**In Vivo**" (standard) and "**In Vitro**" analysis.  
* **Outputs:**  
  * A results table showing the **N-terminal extension**, **peptide**, **C-terminal extension**, and the resulting **peptide IP vs SP** score for each entry.  
  * A button to download the results as a .csv file.

### **3\. Mutation IP vs SP**

* **What it computes:** Calculates a score for one or more mutated peptides, predicting their production preference (IP vs. SP) relative to a list of self-peptides.  
* **Inputs:**  
  * **Mutations (sequence,position):** A list of mutations in the format sequence,position (e.g., PEPTIDESEQ,5). Each entry must be on a new line. A file can also be uploaded.  
  * **Self Peptides (one per line):** A list of self-peptides, one per line. This field is **optional**. A file can also be uploaded.  
* **Outputs:**  
  * A results table showing the **Sequence**, **Mutation Position**, and **Score** for each mutation.  
  * A button to download the results as a .csv file.

### **4\. Tumor IP vs SP**

* **What it computes:** Calculates a single, aggregate score representing the overall tumor-specific immunogenicity potential based on a list of mutations and (optionally) a list of self-peptides.  
* **Inputs:**  
  * **Mutations (sequence,position):** A list of mutations in the format sequence,position (e.g., PEPTIDESEQ,5). Each entry must be on a new line. A file can also be uploaded.  
  * **Self Peptides (one per line):** A list of self-peptides, one per line. This field is **optional**. A file can also be uploaded.  
* **Outputs:**  
  * A single **Tumor Score**.