swt2sw

February 27, 2025 ยท View on GitHub

A tool to convert Spacewalk text-based files (.swt) to Spacewalk binary files (.sw). This format is based on the Hierarchical Data Format (HDF5).

Quick Demo

Try these interactive demos to see how Spacewalk visualizes different data types:

  • Ball & Stick Visualization: Launch Demo
    Shows genomic regions connected by 3D structures, ideal for chromosome conformation data.

  • Point Cloud Visualization: Launch Demo
    Displays multiple spatial points per genomic region, perfect for super-resolution microscopy data.

Installation

Tested with Python 3.12.2

pip install git+https://github.com/jrobinso/hdf5-indexer.git

pip install git+https://github.com/turner/swt2sw.git

Command Line Usage

Convert a text based ball & stick file to a binary format. The use of -single-point indicates the data has a single xyz location for a single genomic extent

swt2sw -f ball-and-stick.swt -n ball-and-stick -single-point

Convert a text based pointcloud file to a binary format. The use of -multi-point indicates the data has multiple xyz location for a single genomic extent

swt2sw -f pointcloud.swt -n pointcloud -multi-point

Documentation

Detailed file format specifications can be found in the Spacewalk Documentation. This documentation includes:

  • Spacewalk Binary File Format (.sw):
    The new, efficient binary format based on HDF5. It offers enhanced performance, improved scalability, and robust support for complex, hierarchical datasets.

  • Legacy Spacewalk Text Format (.swt):
    The original text-based format that is now deprecated. While some legacy files are still in use, it is highly recommended to migrate to the binary format to leverage modern performance improvements and future enhancements.

For comprehensive technical details and migration guidelines, please refer to:

Examples

wget "https://www.dropbox.com/scl/fi/6e0mgljxd9pqo7coi5dy7/ball-and-stick.swt?rlkey=flan64vir2791z78knpotbpcb&st=tfbrqgc3&dl=0" -O ball-and-stick.swt
pip install git+https://github.com/jrobinso/hdf5-indexer.git
pip install git+https://github.com/turner/sw2swb.git
swt2sw -f ball-and-stick.swt -n ball-and-stick -single-point

Google Colab Notebook - Convert CSV data to Spacewalk file

Included in this project is a Google Colab Notebook that is a detailed example of how to convert a simple CSV file to Spacewalk Binary File format. Click this button to run the notebook Open In Colab