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Cooler hic matrix summary starter

Skill ma-compbio-lab/SkillFoundry/skills/epigenomics-and-chromatin/cooler-hic-matrix-summary-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill cooler-hic-matrix-summary-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

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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

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

Keep looking

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