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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: 4 days 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 (over 8 years ago)
Default Branch: develop
Last Pushed: 2024-08-28T16:03:02.000Z (4 months ago)
Last Synced: 2024-12-23T07:05:34.645Z (11 days ago)
Topics: gehlenborglab, hi-c, higlass
Language: Python
Homepage:
Size: 26.9 MB
Stars: 39
Watchers: 14
Forks: 21
Open Issues: 40
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE

Awesome Lists containing this project

README

        # Clodius

[![Python](https://img.shields.io/pypi/v/clodius)](https://pypi.org/project/clodius)

[![Build Status](https://travis-ci.org/higlass/clodius.svg?branch=develop)](https://travis-ci.org/higlass/clodius)

[![Docs](https://img.shields.io/badge/docs-📖-red.svg?colorB=6680ff)](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

```