Final tweaks for flashlfq move: update msgfplus example; remove run "…

…na" setting for mokapot flashlfq
compomics · Sep 5, 2024 · 2fc9552 · 2fc9552
1 parent 205a9ee
commit 2fc9552
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Showing 3 changed files with 2 additions and 27 deletions.
diff --git a/examples/msgfplus-ms2rescore.json b/examples/msgfplus-ms2rescore.json
@@ -7,9 +7,6 @@
         },
         "log_level": "debug",
         "processes": 16,
-        "feature_generators": {
-            "basic": {}
-        },
         "rescoring_engine": {
             "mokapot": {
                 "fasta_file": "examples/proteins/uniprot-proteome-human-contaminants.fasta",

diff --git a/examples/msgfplus-ms2rescore.toml b/examples/msgfplus-ms2rescore.toml
@@ -5,25 +5,7 @@ psm_reader_kwargs = { "score_column" = "PSMScore" }
 log_level = "debug"
 processes = 16
 
-# [ms2rescore.modification_mapping]
-
-# [ms2rescore.fixed_modifications]
-
-[ms2rescore.feature_generators.basic]
-# No options, but setting heading enables feature generator
-
-# [ms2rescore.feature_generators.ms2pip]
-# model = "HCD"
-# ms2_tolerance = 0.02
-
-# [ms2rescore.feature_generators.deeplc]
-# deeplc_retrain = false
-
-# [ms2rescore.feature_generators.maxquant]
-# No options, but setting heading enables feature generator
-
 [ms2rescore.rescoring_engine.mokapot]
 fasta_file = "examples/proteins/uniprot-proteome-human-contaminants.fasta"
 write_weights = true
 write_txt = true
-# write_flashlfq = true
diff --git a/ms2rescore/rescoring_engines/mokapot.py b/ms2rescore/rescoring_engines/mokapot.py
@@ -85,8 +85,8 @@ def rescore(
     if "write_flashlfq" in kwargs:
         _ = kwargs.pop("write_flashlfq")
         logger.warning(
-            "The Mokapot `write_flashlfq` argument has been deprecated. To write FlashLFQ generic "
-            "TSV, use the MS²Rescore-level `write_flashlfq` option instead."
+            "The `write_flashlfq` argument has moved. To write FlashLFQ generic TSV, use the "
+            "MS²Rescore-level `write_flashlfq` option instead."
         )
 
     # Convert PSMList to Mokapot dataset
@@ -166,10 +166,6 @@ def convert_psm_list(
     feature_df.columns = [f"feature:{f}" for f in feature_df.columns]
     combined_df = pd.concat([psm_df[required_columns], feature_df], axis=1)
 
-    # Ensure filename for FlashLFQ txt output
-    if not combined_df["run"].notnull().all():
-        combined_df["run"] = "na"
-
     feature_names = [f"feature:{f}" for f in feature_names] if feature_names else None
 
     lin_psm_data = LinearPsmDataset(