Merge pull request #112 from Proteobench/Module-specific-toml

Module specific toml
Proteobench · Sep 26, 2023 · 60d8ae6 · 60d8ae6
2 parents f65b363 + c796d92
commit 60d8ae6
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Showing 9 changed files with 19 additions and 90 deletions.
diff --git a/proteobench/modules/dda_quant/io_parse_settings/module_settings.toml b/proteobench/modules/dda_quant/io_parse_settings/module_settings.toml
@@ -0,0 +1,12 @@
+[species_expected_ratio]
+[species_expected_ratio.YEAST]
+"1|2" = 2.0
+
+[species_expected_ratio.ECOLI]
+"1|2" = 0.25
+
+[species_expected_ratio.HUMAN]
+"1|2" = 1.0
+
+[general]
+min_count_multispec = 1
diff --git a/proteobench/modules/dda_quant/io_parse_settings/parse_settings_alphapept.toml b/proteobench/modules/dda_quant/io_parse_settings/parse_settings_alphapept.toml
@@ -28,17 +28,6 @@ LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03 = "Condition_B_Sample_Alpha_03"
 "_ECOLI" = "ECOLI"
 "_HUMAN" = "HUMAN"
 
-[species_expected_ratio]
-[species_expected_ratio.YEAST]
-"1|2" = 2.0
-
-[species_expected_ratio.ECOLI]
-"1|2" = 0.25
-
-[species_expected_ratio.HUMAN]
-"1|2" = 1.0
-
 [general]
 contaminant_flag = "Cont_"
 decoy_flag = true
-min_count_multispec = 1
diff --git a/proteobench/modules/dda_quant/io_parse_settings/parse_settings_custom.toml b/proteobench/modules/dda_quant/io_parse_settings/parse_settings_custom.toml
@@ -25,17 +25,6 @@ LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03 = "Condition_B_Sample_Alpha_03"
 "_ECOLI" = "ECOLI"
 "_HUMAN" = "HUMAN"
 
-[species_expected_ratio]
-[species_expected_ratio.YEAST]
-"1|2" = 0.5
-
-[species_expected_ratio.ECOLI]
-"1|2" = 1.5
-
-[species_expected_ratio.HUMAN]
-"1|2" = 1.0
-
 [general]
 contaminant_flag = "Cont_"
 decoy_flag = true
-min_count_multispec = 1
diff --git a/proteobench/modules/dda_quant/io_parse_settings/parse_settings_maxquant.toml b/proteobench/modules/dda_quant/io_parse_settings/parse_settings_maxquant.toml
@@ -26,26 +26,6 @@ LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03 = 2
 "_ECOLI" = "ECOLI"
 "_HUMAN" = "HUMAN"
 
-[species_expected_ratio]
-[species_expected_ratio.YEAST]
-"1|2" = 2.0
-"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01|LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01" = 2.0
-"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02|LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02" = 2.0
-"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03|LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03" = 2.0
-
-[species_expected_ratio.ECOLI]
-"1|2" = 0.25
-"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01|LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01" = 0.25
-"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02|LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02" = 0.25
-"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03|LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03" = 0.25
-
-[species_expected_ratio.HUMAN]
-"1|2" = 1.0
-"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01|LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01" = 1.0
-"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02|LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02" = 1.0
-"LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03|LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03" = 1.0
-
 [general]
 contaminant_flag = "Cont_"
 decoy_flag = true
-min_count_multispec = 1
diff --git a/proteobench/modules/dda_quant/io_parse_settings/parse_settings_msfragger.toml b/proteobench/modules/dda_quant/io_parse_settings/parse_settings_msfragger.toml
@@ -26,17 +26,6 @@ Charge = "Charge"
 "_ECOLI" = "ECOLI"
 "_HUMAN" = "HUMAN"
 
-[species_expected_ratio]
-[species_expected_ratio.YEAST]
-"1|2" = 2.0
-
-[species_expected_ratio.ECOLI]
-"1|2" = 0.25
-
-[species_expected_ratio.HUMAN]
-"1|2" = 1.0
-
 [general]
 contaminant_flag = "Cont_"
 decoy_flag = false
-min_count_multispec = 1
diff --git a/proteobench/modules/dda_quant/io_parse_settings/parse_settings_proline.toml b/proteobench/modules/dda_quant/io_parse_settings/parse_settings_proline.toml
@@ -26,17 +26,6 @@ abundance_DDA_Condition_B_Sample_Alpha_03 = 2
 "_ECOLI" = "ECOLI"
 "_HUMAN" = "HUMAN"
 
-[species_expected_ratio]
-[species_expected_ratio.YEAST]
-"1|2" = 2.0
-
-[species_expected_ratio.ECOLI]
-"1|2" = 0.25
-
-[species_expected_ratio.HUMAN]
-"1|2" = 1.0
-
 [general]
 contaminant_flag = "Cont_"
 decoy_flag = true
-min_count_multispec = 1
diff --git a/proteobench/modules/dda_quant/io_parse_settings/parse_settings_sage.toml b/proteobench/modules/dda_quant/io_parse_settings/parse_settings_sage.toml
@@ -24,17 +24,6 @@
 "_ECOLI" = "ECOLI"
 "_HUMAN" = "HUMAN"
 
-[species_expected_ratio]
-[species_expected_ratio.YEAST]
-"1|2" = 2.0
-
-[species_expected_ratio.ECOLI]
-"1|2" = 0.25
-
-[species_expected_ratio.HUMAN]
-"1|2" = 1.0
-
 [general]
 contaminant_flag = "Cont_"
 decoy_flag = false
-min_count_multispec = 1
diff --git a/proteobench/modules/dda_quant/io_parse_settings/parse_settings_wombat.toml b/proteobench/modules/dda_quant/io_parse_settings/parse_settings_wombat.toml
@@ -2,7 +2,6 @@
 protein_group = "Proteins"
 "modified_peptide" = "Modified sequence"
 
-
 [replicate_mapper]
 abundance_A_1 = 1
 abundance_A_2 = 1
@@ -24,17 +23,6 @@ abundance_B_3 = "Condition_B_Sample_Alpha_03"
 "_ECOLI" = "ECOLI"
 "_HUMAN" = "HUMAN"
 
-[species_expected_ratio]
-[species_expected_ratio.YEAST]
-"1|2" = 2.0
-
-[species_expected_ratio.ECOLI]
-"1|2" = 0.25
-
-[species_expected_ratio.HUMAN]
-"1|2" = 1.0
-
 [general]
 contaminant_flag = "Cont_"
-decoy_flag = true
-min_count_multispec = 1
+decoy_flag = true
diff --git a/proteobench/modules/dda_quant/parse_settings.py b/proteobench/modules/dda_quant/parse_settings.py
@@ -23,6 +23,8 @@
                         "Custom"        : os.path.join(PARSE_SETTINGS_DIR, 'parse_settings_custom.toml')
             }
 
+PARSE_SETTINGS_FILES_MODULE = os.path.join(PARSE_SETTINGS_DIR, 'module_settings.toml')
+
 # ! Could be created from keys of PARSE_SETTINGS_FILES
 INPUT_FORMATS = ("MaxQuant", 
                 "AlphaPept",
@@ -51,8 +53,10 @@ def __init__(self, input_format:str):
         self.decoy_flag = parse_settings["general"]["decoy_flag"]
         self.species_dict = parse_settings["species_mapper"]
         self.contaminant_flag = parse_settings["general"]["contaminant_flag"]
-        self.min_count_multispec = parse_settings["general"]["min_count_multispec"]
-        self.species_expected_ratio = parse_settings["species_expected_ratio"]
+
+        parse_settings_module = toml.load(PARSE_SETTINGS_FILES_MODULE)
+        self.min_count_multispec = parse_settings_module["general"]["min_count_multispec"]
+        self.species_expected_ratio = parse_settings_module["species_expected_ratio"]
 
 
 def parse_settings(input_format:str) -> Settings: