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dataset combine

Combine per-sample QuantNado .zarr stores into a single multi-sample dataset.

Usage

quantnado dataset combine \
  --stores dataset/ATAC_1.zarr dataset/RNA_1.zarr dataset/METH_1.zarr \
  --output dataset/combined.zarr

Required Options

  • --stores: one or more per-sample .zarr stores after a single flag
  • --output, -o: path to the combined multi-sample .zarr

Options

  • --overwrite / --no-overwrite: replace the output store if it already exists
  • --workers, --n-workers: number of thread workers to use while copying rows
  • --log-file PATH: log destination
  • --verbose, -v: debug logging

Notes

  • dataset combine accepts either:
  • one --stores flag followed by a list of store paths, or
  • a single directory path after --stores if you want to combine every .zarr store in that directory
  • incomplete stores are skipped by the combine engine
  • the combined store can be opened with the same QuantNado / QuantNadoDataset API

Example

quantnado dataset combine \
  --stores samples/ATAC_1.zarr samples/H3K27ac_1.zarr samples/RNA_1.zarr \
  --output samples/combined.zarr \
  --workers 4