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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.

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# 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]"
```

## Test Fixtures (Git LFS)

Test data files in `data/` are stored in [Git LFS](https://git-lfs.com/). They are downloaded automatically when you clone the repository with LFS enabled:

```shell
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

1. **Check if the file type is already tracked** — open [.gitattributes](.gitattributes) and look for a matching pattern (e.g. `data/*.gz`, `*.bam`). If not, add a new tracking rule:

```shell
   git lfs track "data/*.ext"   # adds a line to .gitattributes
   git add .gitattributes
   ```

2. **Allow the file through `.gitignore`** — `data/*` is ignored by default. Add a negation line for your file:

```
   !data/your_new_file.ext
   ```

3. **Stage and commit as normal:**

```shell
   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](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
```

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