Add Cross-Replicate Consolidation

[TheLostLambda]

Here are some pointers that I think might help with the implementation!

The goal is to generate an extra, consolidated CSV file when several datasets are uploaded and an "Advanced > Consolidation" option is ticked. If you uploaded three datasets, enabled consolidation, then ran PGFinder, it should download four files. Three of those will be the three it returns now (one CSV file per dataset), and the fourth will be the consolidation of those other three.

The place to loop into this is here: https://github.com/Mesnage-Org/pgfinder/blob/a334000b23fa7a676c0bfb93b40218341e5f7dc7/lib/pgfinder/gui/shim.py#L17-L36

• You add an import from the JS side in the pyio import that stores the bool for whether you should consolidate or not
• Then you check it's true and that you have more than one file in msData
• Then you call the consolidation function on that list of individual CSV outputs
  • You could also change analyze to return a tuple of the original dataframe (matched) as well as the CSV, then you just need to take a DataFrame and don't need to do any more CSV parsing

Writing the actual consolidation function should be relatively straightforward:

1. Stack / vcat the dataframes from each dataset
2. Group by structure
3. Compute mean and stddev for each group (for parameters like intensity and RT)
4. Write into a final table

@smesnage should be able to supply another reference file against which to check this process!

Finally, on the web side, you'll need to add that option to the "Advanced" options for toggling this feature.

1. Add the button to this column of the advanced options: https://github.com/Mesnage-Org/pgfinder/blob/a334000b23fa7a676c0bfb93b40218341e5f7dc7/web/src/routes/AdvancedOptions.svelte#L19-L54
2. Add an exported property representing that boolean button state here, and bind it in the <input> object https://github.com/Mesnage-Org/pgfinder/blob/a334000b23fa7a676c0bfb93b40218341e5f7dc7/web/src/routes/AdvancedOptions.svelte#L5-L10
3. Add a bool to the Pyio type — used to shuttle data from the webUI to PGFinder: https://github.com/Mesnage-Org/pgfinder/blob/a334000b23fa7a676c0bfb93b40218341e5f7dc7/web/src/app.d.ts#L3-L10
4. Bind the boolean property here, connecting the pyio field to the button state in the <AdvancedOptions>: https://github.com/Mesnage-Org/pgfinder/blob/a334000b23fa7a676c0bfb93b40218341e5f7dc7/web/src/routes/%2Bpage.svelte#L117-L124

That should be more than enough to get started with, and I'm happy to guide whoever through the implementation!

[TheLostLambda]

@Ankur-AVP-Patel is being set off on this adventure now, but is waiting on @smesnage for some examples / test cases!

[smesnage]

There it is. Attached is an example of what we are dreaming of. All relevant info (ftrs, database and model output) is in the shared drive: "G:\Shared drives\PG Mass Spec Analysis\PGFinder wishlist\Automation consolidation (for Ankur)" Please @Ankur-AVP-Patel , get in touch if you have any questions!

Cross sample consolidation example_Ankur.xlsx