Closed Jhsmit closed 1 year ago
Hi @ococrook, if you have some time I was wondering if you could give some feedback on the new API and .yaml files as I've reworked them in this PR.
The new .yaml format is as shown here: https://github.com/Jhsmit/PyHDX/blob/refactor_data_loading/tests/test_data/input/data_states.yaml
The other main change is the removal of the PeptideMasterTable
object. Implementation of this part as object-oriented was a poor design decision retrospectively, and I think the new functional approach is much better and makes it easier for users to directly interface with the HDXMeasurement
object. An example of how to use these is here: https://github.com/Jhsmit/PyHDX/blob/a3838a3532d658dd16d50d738999706a694bbc61/templates/01_load_secb_data.py
There are still a few steps in the new procedure related to back-exchange correction that are not very clear in their current implementation and I plan to tackle those in the future.
I'll update the docs shortly.
Large refactoring of how data is loaded into the
HDXMeasurement
object.PeptideMasterTable
object in favor of a functional approach with functionsfilter_peptides
,apply_control
andcorrect_d_uptake
Updated some of the column names in HDX Measurement data: Mapping from old to new column names is:
"start"
->"_start"
"end"
->"_stop"
'_start''
->"start"
"_end"
->'stop'
Additionally, replace spaces in column names with underscores.