Clodius

Displaying large amounts of data often requires first turning it into not-so-large amounts of data. Clodius is a program and library designed to aggregate large datasets to make them easy to display at different resolutions.

Demo

Install the clodius package:

pip install clodius

And use it aggregate a bigWig file:

curl https://raw.githubusercontent.com/hms-dbmi/clodius/develop/test/sample_data/geneAnnotationsExonsUnions.short.bed \
  > /tmp/sample.short.bed
clodius aggregate bedfile /tmp/sample.short.bed

The output files can then be displayed using higlass-manage. For more information about viewing these types of files take a look at the higlass docs.

More examples are available.

File Types

• Non-genomic Rasters
  • TSV Files
• Genomic Data
  • Bed Files
  • BedGraph Files
  • Bedpe-like Files
  • BigBed Files
  • BigWig Files
  • Chromosome Sizes
  • Cooler Files
  • Gene Annotation
  • HiTile Files
  • Multivec Files

Development

The recommended way to develop clodius is to use a conda environment and install clodius with develop mode:

pip install -e ".[dev]"

Testing

The unit tests for clodius can be run using pytest:

pytest

Individual unit tests can be specified by indicating the file and function they are defined in:

pytest test/cli_test.py:test_clodius_aggregate_bedgraph