https://github.com/higlass/clodius
Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.
https://github.com/higlass/clodius
gehlenborglab hi-c higlass
Last synced: about 1 year ago
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Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.
- Host: GitHub
- URL: https://github.com/higlass/clodius
- Owner: higlass
- License: mit
- Created: 2016-04-22T13:20:09.000Z (about 10 years ago)
- Default Branch: develop
- Last Pushed: 2025-02-22T05:33:03.000Z (over 1 year ago)
- Last Synced: 2025-03-29T07:05:29.791Z (about 1 year ago)
- Topics: gehlenborglab, hi-c, higlass
- Language: Python
- Homepage:
- Size: 26.9 MB
- Stars: 39
- Watchers: 13
- Forks: 21
- Open Issues: 40
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# Clodius
[](https://pypi.org/project/clodius)
[](https://travis-ci.org/higlass/clodius)
[](https://docs.higlass.io/data_preparation.html)
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:
```shell
pip install clodius
```
And use it aggregate a bigWig file:
```shell
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](https://github.com/higlass/higlass-manage). For more information about viewing these types of files take a look at the [higlass docs](https://docs.higlass.io).
[More examples](COMMANDS.md) are available.
## File Types
- Non-genomic Rasters
- [TSV Files](docs/raster/tsv.rst)
- Genomic Data
- [Bed Files](docs/genomic/bed.rst)
- [BedGraph Files](docs/genomic/bedgraph.rst)
- [Bedpe-like Files](docs/genomic/bedpe.rst)
- [BigBed Files](docs/genomic/bigbed.rst)
- [BigWig Files](docs/genomic/bigwig.rst)
- [Chromosome Sizes](docs/genomic/chromosome-sizes.rst)
- [Cooler Files](docs/genomic/cooler.rst)
- [Gene Annotation](docs/genomic/gene-annotation.rst)
- [HiTile Files](docs/genomic/hitile.rst)
- [Multivec Files](docs/genomic/multivec.rst)
## Development
The recommended way to develop `clodius` is to use a [conda](https://conda.io/docs/intro.html) environment and
install `clodius` with develop mode:
```shell
pip install -e ".[dev]"
```
## Testing
The unit tests for clodius can be run using [pytest](https://docs.pytest.org/en/latest/):
```shell
pytest
```
Individual unit tests can be specified by indicating the file and function
they are defined in:
```shell
pytest test/cli_test.py:test_clodius_aggregate_bedgraph
```