tcga-downloader/examples

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

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

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

python examples/advanced_filtering.py

4. Using Configuration Files

File: using_config.py

Demonstrates:

• Creating a default configuration file
• Using configuration for other commands

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

python examples/validate_downloads.py

Running Examples

Make sure you have TCGA Downloader installed:

pip install -e .

Then run any example:

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:

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:

tcga-downloader interactive --out manifest.tsv --out-dir ./data

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