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# cooler Hi-C Matrix Summary Starter
Use this skill to generate or inspect a tiny Hi-C contact matrix in Cooler format and summarize its bins and pixel counts in JSON.
## What it does
- Creates a deterministic toy `.cool` file with three bins and five nonzero upper-triangle pixels.
- Opens the Cooler store with `cooler.Cooler` and summarizes matrix shape, pixel count, and total contact count.
- Can also summarize an existing Cooler file if `--input` is provided.
## When to use it
- You need a runnable starter for Hi-C contact matrix formats.
- You want a small verified example before building larger chromatin-interaction workflows.
- You need a smoke-testable wrapper around `cooler` in the repo-managed scientific Python environment.
## Example
```bash
slurm/envs/scientific-python/bin/python skills/epigenomics-and-chromatin/cooler-hic-matrix-summary-starter/scripts/run_cooler_hic_matrix_summary.py \
--out scratch/epigenomics/cooler_hic_summary.json \
--cooler-out scratch/epigenomics/toy_contacts.cool
```
## Verification
- Skill-local tests: `python3 -m unittest discover -s skills/epigenomics-and-chromatin/cooler-hic-matrix-summary-starter/tests -p 'test_*.py'`
- Expected summary: `bin_count == 3`, `pixel_count == 5`, and `total_contact_count == 38`
