Open vrkosk opened 3 months ago
Hi, @vrkosk,
Thanks for reporting! We will look into this.
Best, Ralf
For internal reference:
_psm_list_to_deeplc_peprec()
has already been removed in the timsRescore
branch in favor of sending the PSMList directly to DeepLC. However, we should still look into how this behaves when there are not enough PSMs (or none) for calibration.
I'm getting an uncaught exception when trying to use ms2rescore.feature_generators.ms2pip.DeepLCFeatureGenerator. The error happens when there are not enough peptides in psm_list for the calibration set.
Here's how I create the environment:
I'm calling the feature generator as instructed in MS2Rescore docs:
When there are only a few items in psm_list, there's an uncaught exception:
The workaround in my script is to pass
calibration_set_size=1.0
whenround(calibration_set_size * len(psm_list[~psm_list['is_decoy']])) == 0
. Then _psm_list_to_deeplc_peprec() gets a non-empty array and all is fine. Quite likely I shouldn't even use DeepLC if there aren't enough peptide matches!