fix test errors after adding parameter

Proteobench · Jan 17, 2025 · d822f61 · d822f61
1 parent 3b659b4
commit d822f61
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Showing 26 changed files with 34 additions and 7 deletions.
diff --git a/.gitignore b/.gitignore
@@ -142,3 +142,6 @@ results.json
 
 # secrets
 **/.streamlit/secrets.toml
+
+# wew
+build.sh
diff --git a/proteobench/io/params/alphapept.py b/proteobench/io/params/alphapept.py
@@ -66,7 +66,7 @@ def extract_params(fname: pathlib.Path) -> ProteoBenchParameters:
     params.min_precursor_charge = record["features"]["iso_charge_min"]
     params.max_precursor_charge = record["features"]["iso_charge_max"]
     params.enable_match_between_runs = record["workflow"]["match"]  # Check if matching is enabled
-
+    params.abundance_normalization_ions = None  # No normalization in AlphaPept
     return params
 
 

diff --git a/proteobench/io/params/diann.py b/proteobench/io/params/diann.py
@@ -346,7 +346,7 @@ def extract_params(fname: str) -> ProteoBenchParameters:
 
     # If scan window is not customely set, extract it from the log file
     parameters["scan_window"] = int(extract_with_regex(lines, scan_window_regex))
-
+    parameters["abundance_normalization_ions"] = None
     return ProteoBenchParameters(**parameters)
 
 

diff --git a/proteobench/io/params/fragger.py b/proteobench/io/params/fragger.py
@@ -156,10 +156,13 @@ def extract_params(file: BytesIO) -> ProteoBenchParameters:
         params.ident_fdr_protein = fragpipe_params.loc["ionquant.proteinfdr"]
         params.ident_fdr_peptide = fragpipe_params.loc["ionquant.peptidefdr"]
         params.ident_fdr_psm = fragpipe_params.loc["ionquant.ionfdr"]
+        params.abundance_normalization_ions = fragpipe_params.loc["ionquant.normalization"]
+
     elif fragpipe_params.loc["diann.run-dia-nn"] == "true":
         params.ident_fdr_protein = fragpipe_params.loc["diann.q-value"]
         params.ident_fdr_peptide = fragpipe_params.loc["diann.q-value"]
         params.ident_fdr_psm = fragpipe_params.loc["diann.q-value"]
+        params.abundance_normalization_ions = None
 
     # Precursor charge settings
     if fragpipe_params.loc["msfragger.override_charge"] == "true":

diff --git a/proteobench/io/params/spectronaut.py b/proteobench/io/params/spectronaut.py
@@ -128,7 +128,7 @@ def read_spectronaut_settings(file_path: str) -> ProteoBenchParameters:
     params.second_pass = extract_value(lines, "directDIA Workflow:")
     params.protein_inference = extract_value(lines, "Inference Algorithm:")  # or Protein Inference Workflow:
     params.predictors_library = extract_value(lines, "Hybrid (DDA + DIA) Library").replace(":", "").strip()
-
+    params.abundance_normalization_ions = extract_value(lines, "Cross-Run Normalization:")
     return params
 
 

diff --git a/test/params/DIANN_1.7.16.log.csv b/test/params/DIANN_1.7.16.log.csv
@@ -23,3 +23,4 @@ quantification_method,QuantUMS high-precision
 second_pass,False
 protein_inference,
 predictors_library,"{'RT': 'DIANN', 'IM': 'DIANN', 'MS2_int': 'DIANN'}"
+abundance_normalization_ions,
diff --git a/test/params/DIANN_WU304578_report.log.csv b/test/params/DIANN_WU304578_report.log.csv
@@ -23,3 +23,4 @@ quantification_method,QuantUMS high-precision
 second_pass,False
 protein_inference,
 predictors_library,"{'RT': 'DIANN', 'IM': 'DIANN', 'MS2_int': 'DIANN'}"
+abundance_normalization_ions,
diff --git a/test/params/DIANN_output_20240229_report.log.csv b/test/params/DIANN_output_20240229_report.log.csv
@@ -23,3 +23,4 @@ quantification_method,QuantUMS high-accuracy
 second_pass,True
 protein_inference,Protein_names
 predictors_library,"{'RT': 'DIANN', 'IM': 'DIANN', 'MS2_int': 'DIANN'}"
+abundance_normalization_ions,
diff --git a/test/params/ProlineStudio_241024.csv b/test/params/ProlineStudio_241024.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,
 predictors_library,
+abundance_normalization_ions,
diff --git a/test/params/ProlineStudio_withMBR.csv b/test/params/ProlineStudio_withMBR.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,
 predictors_library,
+abundance_normalization_ions,
diff --git a/test/params/Proline_example_2.csv b/test/params/Proline_example_2.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,
 predictors_library,
+abundance_normalization_ions,
diff --git a/test/params/Proline_example_w_Mascot_wo_proteinSets.csv b/test/params/Proline_example_w_Mascot_wo_proteinSets.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,
 predictors_library,
+abundance_normalization_ions,
diff --git a/test/params/Version1_9_Predicted_Library_report.log.csv b/test/params/Version1_9_Predicted_Library_report.log.csv
@@ -23,3 +23,4 @@ quantification_method,QuantUMS high-precision
 second_pass,True
 protein_inference,Protein_names
 predictors_library,"{'RT': 'DIANN', 'IM': 'DIANN', 'MS2_int': 'DIANN'}"
+abundance_normalization_ions,
diff --git a/test/params/alphapept_0.4.9.csv b/test/params/alphapept_0.4.9.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,
 predictors_library,
+abundance_normalization_ions,
diff --git a/test/params/alphapept_0.4.9_unnormalized.csv b/test/params/alphapept_0.4.9_unnormalized.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,
 predictors_library,
+abundance_normalization_ions,
diff --git a/test/params/fragpipe_extracted_params.csv b/test/params/fragpipe_extracted_params.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,ProteinProphet: --maxppmdiff 2000000
 predictors_library,
+abundance_normalization_ions,1
diff --git a/test/params/fragpipe_v22_extracted_params.csv b/test/params/fragpipe_v22_extracted_params.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,ProteinProphet: --maxppmdiff 2000000
 predictors_library,
+abundance_normalization_ions,1
diff --git a/test/params/fragpipe_win_paths_extracted_params.csv b/test/params/fragpipe_win_paths_extracted_params.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,ProteinProphet: --maxppmdiff 2000000
 predictors_library,
+abundance_normalization_ions,1
diff --git a/test/params/i2mproteobench_2pep_fdr01psm_fdr01prot_xtandem_sel.csv b/test/params/i2mproteobench_2pep_fdr01psm_fdr01prot_xtandem_sel.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,
 predictors_library,
+abundance_normalization_ions,
diff --git a/test/params/i2mproteobench_params_sage_sel.csv b/test/params/i2mproteobench_params_sage_sel.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,
 predictors_library,
+abundance_normalization_ions,
diff --git a/test/params/i2mq_result_parameters_sel.csv b/test/params/i2mq_result_parameters_sel.csv
@@ -23,3 +23,4 @@ quantification_method,
 second_pass,
 protein_inference,
 predictors_library,
+abundance_normalization_ions,
diff --git a/test/params/mqpar1.5.3.30_MBR_sel.json b/test/params/mqpar1.5.3.30_MBR_sel.json
@@ -22,5 +22,6 @@
     "quantification_method": null,
     "second_pass": null,
     "protein_inference": null,
-    "predictors_library": null
+    "predictors_library": null,
+    "abundance_normalization_ions": null
 }
diff --git a/test/params/mqpar_MQ1.6.3.3_MBR_sel.json b/test/params/mqpar_MQ1.6.3.3_MBR_sel.json
@@ -22,5 +22,6 @@
     "quantification_method": null,
     "second_pass": null,
     "protein_inference": null,
-    "predictors_library": null
+    "predictors_library": null,
+    "abundance_normalization_ions": null
 }
diff --git a/test/params/mqpar_MQ2.1.3.0_noMBR_sel.json b/test/params/mqpar_MQ2.1.3.0_noMBR_sel.json
@@ -22,5 +22,6 @@
     "quantification_method": null,
     "second_pass": null,
     "protein_inference": null,
-    "predictors_library": null
+    "predictors_library": null,
+    "abundance_normalization_ions": null
 }
diff --git a/test/params/mqpar_mq2.6.2.0_1mc_MBR_sel.json b/test/params/mqpar_mq2.6.2.0_1mc_MBR_sel.json
@@ -22,5 +22,6 @@
     "quantification_method": null,
     "second_pass": null,
     "protein_inference": null,
-    "predictors_library": null
+    "predictors_library": null,
+    "abundance_normalization_ions": null
 }
diff --git a/test/params/spectronaut_Experiment1_ExperimentSetupOverview_BGS_Factory_Settings.csv b/test/params/spectronaut_Experiment1_ExperimentSetupOverview_BGS_Factory_Settings.csv
@@ -23,3 +23,4 @@ quantification_method,MS2
 second_pass,directDIA+ (Deep)
 protein_inference,IDPicker
 predictors_library,False
+abundance_normalization_ions,True