# Examples

This directory contains example scripts demonstrating various use cases of TCGA Downloader.

## Examples

### 1. Basic Query and Download

**File:** `basic_query_download.py`

Demonstrates:
- Querying a single TCGA project
- Creating a manifest file
- Downloading files using the manifest

```bash
python examples/basic_query_download.py
```

### 2. Batch Query Multiple Projects

**File:** `batch_query.py`

Demonstrates:
- Querying multiple TCGA projects in one command
- Combining results from multiple queries
- Statistics for combined results

```bash
python examples/batch_query.py
```

### 3. Advanced Filtering

**File:** `advanced_filtering.py`

Demonstrates:
- Querying with sample type filter
- Querying with platform filter
- Multiple filter criteria at once

```bash
python examples/advanced_filtering.py
```

### 4. Using Configuration Files

**File:** `using_config.py`

Demonstrates:
- Creating a default configuration file
- Using configuration for other commands

```bash
python examples/using_config.py
tcga-downloader query --file config.json
```

### 5. Validate Downloads

**File:** `validate_downloads.py`

Demonstrates:
- Loading a manifest file
- Validating manifest structure
- Checking downloaded files against manifest
- Verifying MD5 checksums

```bash
python examples/validate_downloads.py
```

## Running Examples

Make sure you have TCGA Downloader installed:

```bash
pip install -e .
```

Then run any example:

```bash
cd examples
python <example_name>.py
```

## Common TCGA Projects

- TCGA-BRCA: Breast invasive carcinoma
- TCGA-LUAD: Lung adenocarcinoma
- TCGA-COAD: Colon adenocarcinoma
- TCGA-PRAD: Prostate adenocarcinoma
- TCGA-SKCM: Skin cutaneous melanoma
- TCGA-KIRC: Kidney renal clear cell carcinoma
- TCGA-GBM: Glioblastoma multiforme

## Common Data Types

- Gene Expression
- Copy Number Variation
- DNA Methylation
- miRNA Expression
- Protein Expression
- Somatic Mutation

## Interactive Mode

**File:** `interactive_example.py`

Demonstrates:
- Dynamic project selection from API
- Dynamic data type selection based on selected project
- Interactive menu-driven workflow

Usage:
```bash
tcga-downloader interactive --out manifest.tsv --out-dir ./data
```

The interactive mode provides a user-friendly menu-driven workflow:

1. **Dynamic Project List**: Fetches available TCGA projects from GDC API
2. **Project Selection**: Interactive menu to select a project
3. **Dynamic Data Types**: Fetches available data types for selected project
4. **Data Type Selection**: Interactive menu to select data type
5. **Manifest Generation**: Creates manifest based on selections
6. **Download**: Downloads files using gdc-client

Usage:
```bash
tcga-downloader interactive --out manifest.tsv --out-dir ./data
```

This mode requires `questionary` library, which is included in the main package dependencies.