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Add CytoTable module to have csv and npz support #43

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axiomcura opened this issue Apr 11, 2023 · 0 comments
Open

Add CytoTable module to have csv and npz support #43

axiomcura opened this issue Apr 11, 2023 · 0 comments
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enhancement New feature or request

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axiomcura commented Apr 11, 2023

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 #37 (comment)

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 #37 (comment)

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

@axiomcura axiomcura added the enhancement New feature or request label Apr 11, 2023
@axiomcura axiomcura self-assigned this Apr 11, 2023
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