--apply_weights requires --ss_main_score to be specified as in the original command

[jcharkow]

I get unexpected results when using --apply_weights with XGBoost if a --ss_main_score was set manually.

E.g.

pyprophet score --in in.oswpq --level=ms1ms2 --classifier=XGBoost --ss_main_score=var_dotprod_score

• Trains the model as expected

However if this command is used
pyprophet score --in in.oswpq --level=ms1ms2 --classifier=XGBoost --apply_weights=weights.bin

The weights are applied to the incorrect scores

(Same weights on different columns)

To get the expected results the --ss_main_score has to be specified as in the original run
pyprophet score --in in.oswpq --level=ms1ms2 --classifier=XGBoost --ss_main_score=var_dotprod_score --apply_weights=weights.bin

It would be nice if this was detected automatically somehow

[singjc]

I think keeping track of the feature names, something similar to the draft PR #117, would probably be able to make this automatic. Need to check if the issue is the same with the other models, and file types.