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Jhsmit / PyHDX

Derive ΔG for single residues from HDX-MS data
http://pyhdx.readthedocs.io
MIT License
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HDExaminer conversion and allow replicates #350

Open tuttlelm opened 2 weeks ago

tuttlelm commented 2 weeks ago

models.py Changes were made to the HDXMeasurement init function to allow the original HDX-MS data to contain replicates. HDExaminer output can contain either summary data for every fit spectrum or replicate averaged data. This change allows creation of the HDXMeasurement object from either type of data.

convert_data.py Function to convert the summary uptake table output from HDExaminer to a format usable by pyhdx. This primarily involves mapping column names, but will sometimes require dummy values (e.g. if rfu_sd is missing, a 5% error value is assumed)

Jhsmit commented 2 weeks ago

Thanks for the PR!

Unfortunately it look like some of changes to models.py cause issues for the web application part of PyHDX . I'll try to take a look but I'm not sure if I'll have time soon due to holidays.

If you have an example 'all_results.csv' file that would be very helpful so we can add automated tests. It doesnt have to be real data, just as long as the format is correct we can use it for testing.

tuttlelm commented 1 day ago

Unfortunate that it breaks things in the web interface. I have only used pyHDX functions in a Jupyter Notebook. I've added a couple example HDExaminer outputs in HDExaminer_examples. You can see that the HDExaminer outputs aren't even self-consistent in column labels. Both formats are handled by the convert_data.py function.