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

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