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# Scanpy DPT Trajectory Starter
Use this skill to compute a deterministic toy diffusion-pseudotime trajectory with Scanpy `tl.dpt`.
## What it does
- Loads a tiny genes-by-cells matrix and a root cell.
- Builds a Scanpy neighbors graph, computes diffusion components, and runs `tl.dpt`.
- Exports per-cell pseudotime values and the inferred cell order.
## When to use it
- You need a verified starter for the `trajectory inference` leaf in transcriptomics.
- You want a bounded example of DPT before moving to larger pseudotime workflows.
- You need deterministic JSON output that can be checked in repository tests.
## Example
```bash
slurm/envs/scanpy/bin/python skills/transcriptomics/scanpy-dpt-trajectory-starter/scripts/run_scanpy_dpt_trajectory.py \
--counts skills/transcriptomics/scanpy-dpt-trajectory-starter/examples/toy_counts.tsv \
--root-cell c0 \
--expected-order skills/transcriptomics/scanpy-dpt-trajectory-starter/examples/expected_order.txt \
--summary-out scratch/scanpy-dpt/summary.json
```
## Verification
- Skill-local tests: `python3 -m unittest discover -s skills/transcriptomics/scanpy-dpt-trajectory-starter/tests -p 'test_*.py'`
- Expected summary: the inferred order equals `c0..c5` and pseudotime increases monotonically from `0.0` to `1.0`
