download-encodelisted

# Download ENCODE Files ## When to Use - User wants to download ENCODE data files to their local machine - User asks to "download", "get", or "fetch" ENCODE files - User needs specific file formats (BED, FASTQ, BAM, bigWig) from experiments - User wants to batch download files matching search criteria - User needs to verify file integrity after download (MD5 checksums) - User asks about organizing downloaded files by experiment or format Help the user download ENCODE data files to their local machine. ## Download Strategy 1. **Specific files by accession**: Use `encode_download_files` with file accession IDs (e.g., "ENCFF635JIA"). 2. **Batch download by criteria**: Use `encode_batch_download` to search and download in one step. - Always start with `dry_run=True` (default) to preview what will be downloaded - Show the user the file count, total size, and file list - Only proceed with `dry_run=False` after user confirms 3. **Download organization options**: - `"flat"`: All files in one directory - `"experiment"`: Organized by experiment accession (recommended) - `"format"`: Organized by file format - `"experiment_format"`: Organized by experiment, then format ## Important Notes - All downloads include MD5 verification by default (`verify_md5=True`) - Ask the user for a download directory if not specified - Warn about large downloads (>1GB total or >50 files) - Files already downloaded will be skipped (idempotent) - For restricted files, credentials