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WayScience / CytoSnake

Orchestrating high-dimensional cell morphology data processing pipelines
https://cytosnake.readthedocs.io
Creative Commons Attribution 4.0 International
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Add `CytoTable` module to have `csv` and `npz` support #43

Open axiomcura opened 1 year ago

axiomcura commented 1 year ago

What other formats might you want to use with CytoSnake? If CytoSnake will be tightly coupled with the SQLite format, consider providing those details upfront via documentation.

_Originally posted by @d33bs in https://github.com/WayScience/CytoSnake/pull/37#discussion_r1162982096_

CytoTable does not only convert sqlite to parquet files but also npz (DeepProfiler) and csv (CellProfiler)

Currently the CytoTable module in CytoSnake only takes sqlite files as input.

@axiomcura , @gwaybio - Yes, this is correct. CytoTable will attempt to navigate a provided source data directory for nested CSV's or SQLite data and concatenate or join the data together in the results.

_Originally posted by @d33bs in https://github.com/WayScience/CytoSnake/pull/37#discussion_r1163027988_

CytoTable expects CSV files to be within a directory while CytoTable expects NPZ files to only be a file path