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

Development

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

pip install -e ".[dev]"

Test Fixtures (Git LFS)

Test data files in data/ are stored in Git LFS. They are downloaded automatically when you clone the repository with LFS enabled:

git lfs install  # once per machine
git clone <repo>  # LFS files downloaded automatically
# or, in an existing clone:
git lfs pull

Adding a new test fixture

Check if the file type is already tracked — open .gitattributes and look for a matching pattern (e.g. data/*.gz, *.bam). If not, add a new tracking rule:
```
git lfs track "data/*.ext"   # adds a line to .gitattributes
git add .gitattributes
```
Allow the file through .gitignore — data/* is ignored by default. Add a negation line for your file:
```
!data/your_new_file.ext
```

Stage and commit as normal:

git add data/your_new_file.ext
git commit -m "Add test fixture: your_new_file.ext"
git push  # LFS objects are uploaded automatically

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

Release files for clodius 0.22.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for clodius 0.22.2
File	Size	Uploaded
clodius-0.22.2.tar.gz	11.7 MB	Apr 20, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for clodius 0.22.2
File	Interpreter	ABI	Platform	Reset
clodius-0.22.2-py3-none-any.whl 125.2 kB Apr 20, 2026	Python 3	none	any	Details

Total release size: 11.8 MB

Release files / clodius-0.22.2.tar.gz

Download URL	clodius-0.22.2.tar.gz
Size	11.7 MB
Tags	Source
SHA-256 checksum How to use checksums	`3e890483b3b8df3e89a70838ce0dceb2652721da0acc3556c5cf6706a2c7ec32`
BLAKE2b-256 checksum How to use checksums	`79c1c1c4f9a177f74d984fb831ad57b83b08331effc47c2a127c8515a1658a39`
Upload date	Apr 20, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.9.25`

Release files / clodius-0.22.2-py3-none-any.whl

Download URL	clodius-0.22.2-py3-none-any.whl
Size	125.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`e4fdf1f6d8d463e89dcac59abe37ea43bf4984dbd5c9e64316ede1cf88c0b2c1`
BLAKE2b-256 checksum How to use checksums	`4844092f6f73eb6b65909280c8ea9dc91d74f58378e9bd6a7be8d2df2e833672`
Upload date	Apr 20, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.9.25`