Legacy Spacewalk Text Format

The legacy text-based format (.swt) is now deprecated. Use the swt2sw tool to migrate to the new .sw format.

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