Ready for v0.2.7

kusterlab · Aug 12, 2022 · c2e7aff · c2e7aff
1 parent c7bb0f4
commit c2e7aff
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Showing 7 changed files with 327 additions and 202 deletions.
diff --git a/.gitignore b/.gitignore
@@ -130,3 +130,4 @@ dmypy.json
 
 system*
 data*
+results*
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,3 +1,6 @@
+v0.2.7
+- Added maxtasksperchild for better memory management in LFQ
+
 v0.2.6
 - Upgrade minimum Python version to 3.8 for new scipy version
 - Reduced LFQ memory by 80% and speed up by 30%

diff --git a/picked_group_fdr/methods.py b/picked_group_fdr/methods.py
@@ -8,7 +8,7 @@ def get_methods(args):
   ### WELL-CALIBRATED METHODS
 
   # final method
-  configs.append({'pickedStrategy' : PickedGroupStrategy(), 'scoreType' : ProteinScoringStrategy("bestPEP"), 'grouping' : RescuedSubsetGrouping()})
+  configs.append({'pickedStrategy' : PickedGroupStrategy(), 'scoreType' : ProteinScoringStrategy("bestPEP"), 'grouping' : RescuedSubsetGrouping(), 'label' : 'Picked Protein Group FDR'})
 
   # picked FDR
   # N.B. Add "remap" to the scoreType if the fasta database used for protein grouping is different from the one used by Percolator
@@ -103,6 +103,15 @@ def get_methods(args):
   #configs.append({'pickedStrategy' : PickedGroupStrategy(), 'scoreType' : ProteinScoringStrategy("Perc bestPEP"), 'grouping' : RescuedSubsetGrouping(), 'label' : 'Picked Protein Group FDR' })
 
 
+  #configs.append({'pickedStrategy' : ClassicStrategy(), 'scoreType' : ProteinScoringStrategy("multPEP razor"), 'grouping' : SubsetGrouping(), 'label' : 'MaxQuant' })
+  #configs.append({'pickedStrategy' : ClassicStrategy(), 'scoreType' : ProteinScoringStrategy("Perc remap multPEP razor"), 'grouping' : SubsetGrouping(), 'label' : 'MaxQuant Perc PEP' })
+  #configs.append({'pickedStrategy' : PickedGroupStrategy(), 'scoreType' : ProteinScoringStrategy("multPEP razor"), 'grouping' : SubsetGrouping(), 'label' : 'MaxQuant picked' })
+  #configs.append({'pickedStrategy' : PickedGroupStrategy(), 'scoreType' : ProteinScoringStrategy("Perc remap multPEP razor"), 'grouping' : SubsetGrouping(), 'label' : 'MaxQuant Perc PEP picked' })
+  #configs.append({'pickedStrategy' : PickedGroupStrategy(), 'scoreType' : ProteinScoringStrategy("Perc remap multPEP razor"), 'grouping' : RescuedSubsetGrouping(), 'label' : 'MaxQuant Perc PEP picked rescued' })
+  #configs.append({'pickedStrategy' : ClassicStrategy(), 'scoreType' : ProteinScoringStrategy("Perc remap bestPEP"), 'grouping' : RescuedSubsetGrouping(), 'label' : 'Classic Protein Group FDR'})
+  #configs.append({'pickedStrategy' : PickedGroupStrategy(), 'scoreType' : ProteinScoringStrategy("Perc remap bestPEP"), 'grouping' : RescuedSubsetGrouping(), 'label' : 'Picked Protein Group FDR'})
+
+
   #################
   ### Figure 5D ###
   #################