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.
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.
The recommended way to develop clodius is to use a conda environment and
install clodius with develop mode:
pip install -e ".[dev]"
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
FAQs
Tile generation for big data
We found that clodius demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
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