From 8225d1d6c4478c93902be1320a76317cf858ec2e Mon Sep 17 00:00:00 2001 From: rodvrees Date: Tue, 11 Mar 2025 09:56:03 +0100 Subject: [PATCH] Add ion mobility prediction option and update comments for clarity --- ms2pip/_utils/ion_mobility.py | 2 +- ms2pip/_utils/retention_time.py | 4 ++-- ms2pip/core.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/ms2pip/_utils/ion_mobility.py b/ms2pip/_utils/ion_mobility.py index 8a3764b1..2ee91fa2 100644 --- a/ms2pip/_utils/ion_mobility.py +++ b/ms2pip/_utils/ion_mobility.py @@ -27,6 +27,6 @@ def add_im_predictions(self, psm_list: PSMList) -> None: """Add ion mobility predictions to the PSMList.""" logger.info("Predicting ion mobility...") predictions: pd.Series = self.predict_fn( - psm_list, write_output=False, n_jobs=self.processes + psm_list, write_output=False, n_jobs=self.processes, ion_mobility=True ) psm_list["ion_mobility"] = predictions.values diff --git a/ms2pip/_utils/retention_time.py b/ms2pip/_utils/retention_time.py index 043f24a2..a1015a25 100644 --- a/ms2pip/_utils/retention_time.py +++ b/ms2pip/_utils/retention_time.py @@ -104,7 +104,7 @@ def _prepare_deeplc_peptide_df(self): """ column_map = {"peptide": "seq", "modifications": "modifications"} peprec = peptide_record.to_dataframe(self.psm_list)[column_map.keys()] - self.deeplc_pep_df = peprec.rename(columns=column_map) + self.deeplc_pep_df = peprec.rename(columns=column_map) #TODO: allow PSMList input def _run_deeplc(self): """Run DeepLC.""" @@ -133,7 +133,7 @@ def add_rt_predictions(self, psm_list): """ self.psm_list = psm_list - if self.predictor == "deeplc": + if self.predictor == "deeplc": #TODO: throw out self._predict_deeplc() else: raise NotImplementedError(self.predictor) diff --git a/ms2pip/core.py b/ms2pip/core.py index f3dd5ec0..d8999a18 100644 --- a/ms2pip/core.py +++ b/ms2pip/core.py @@ -199,7 +199,7 @@ def predict_library( logging.disable(logging.CRITICAL) yield predict_batch( search_space.filter_psms_by_mz(PSMList(psm_list=list(batch))), - add_retention_time=add_retention_time, + add_retention_time=add_retention_time, #TODO: Perhaps get calibrated DeepLC instance out of predict_batch add_ion_mobility=add_ion_mobility, model=model, model_dir=model_dir,