Legacy Spacewalk Text Format

The legacy text-based format (.swt) is no longer supported by Spacewalk. Use the swt2sw tool to convert legacy .swt files to the .sw HDF5 format before loading.

Format Specification

File Structure

1. First Line: Format directive with key-value properties
   • Format specifier (required)
   • Name (required)
   • Genome identifier (required, e.g., hg38, GRCh38)

2. Second Line: Six column headings, whitespace-delimited

3. Remaining Lines: Blocks of trace data
   • Each block begins with a “trace” line
   • Followed by data lines
   • All tokens are whitespace delimited

Example Formats

Ball & Stick Data (ORCA)

Each record links a geometric location with a genomic range:

Point Cloud Data (OligoSTORM)

Multiple geometric locations can share the same genomic range:

Migration

To convert legacy .swt files to the new .sw format:

1. Install the migration tool:

   pip install swt2sw
   

2. Convert your files:

   swt2sw input.swt output.sw