From 1035124b854e21998d3fd9de4935780a19a2d3d3 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 10 Oct 2019 18:08:44 +0200
Subject: Makefile update, obsolete scripts removed

---
 Makefile | 57 +++++++++++++++++++++++++++++++--------------------------
 1 file changed, 31 insertions(+), 26 deletions(-)

(limited to 'Makefile')

diff --git a/Makefile b/Makefile
index 47c6aad..421d75e 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
 # Manuscript
-# please install pandoc-scholar (https://github.com/pandoc-scholar/pandoc-scholar) in the pandoc-scholar directory or point PANDOC_SCHOLAR_PATH to tour installation
+# please install pandoc-scholar (https://github.com/pandoc-scholar/pandoc-scholar) in the pandoc-scholar directory or point PANDOC_SCHOLAR_PATH to your installation
 
 ARTICLE_FILE          = mutagenicity.md
 PANDOC_SCHOLAR_PATH   = pandoc-scholar
@@ -13,7 +13,13 @@ include $(PANDOC_SCHOLAR_PATH)/Makefile
 
 # Lazar
 
-LAZAR_DIR = "../lazar" 
+LAZAR_DIR = ../lazar
+LAZAR_MODEL_DIR = $(LAZAR_DIR)/models/mutagenicity
+LAZAR_PADEL_MODEL_DIR = $(LAZAR_DIR)/models/mutagenicity-padel
+LAZAR_SUMMARY_DIR = $(LAZAR_MODEL_DIR)/crossvalidation/summaries
+LAZAR_PADEL_SUMMARY_DIR = $(LAZAR_PADEL_MODEL_DIR)/crossvalidation/summaries
+LAZAR_CONFUSION_MATRIX_DIR = $(LAZAR_MODEL_DIR)/crossvalidation/confusion_matrices
+LAZAR_PADEL_CONFUSION_MATRIX_DIR = $(LAZAR_PADEL_MODEL_DIR)/crossvalidation/confusion_matrices
 
 # Experiments
 
@@ -21,16 +27,17 @@ SUMMARIES_DIR = 10-fold-crossvalidations/summaries
 CONFUSION_MATRICES_DIR = 10-fold-crossvalidations/confusion-matrices
 R_CV_DIR = 10-fold-crossvalidations/R
 TENSORFLOW_CV_DIR = 10-fold-crossvalidations/tensorflow
-LAZAR_CV_DIR = 10-fold-crossvalidations/lazar
 
 #tables = tables/R-SVM.csv tables/R-RF.csv tables/R-DL.csv
 
-SUMMARIES = $(SUMMARIES_DIR)/R-SVM.csv $(SUMMARIES_DIR)/R-RF.csv $(SUMMARIES_DIR)/R-DL.csv $(SUMMARIES_DIR)/tensorflow-all.csv $(SUMMARIES_DIR)/tensorflow-selected.csv $(SUMMARIES_DIR)/lazar-all.csv $(SUMMARIES_DIR)/lazar-high-confidence.csv
-# TODO lazar model/cv with PaDEL descriptors
+SUMMARIES = $(SUMMARIES_DIR)/R-SVM.csv $(SUMMARIES_DIR)/R-RF.csv $(SUMMARIES_DIR)/R-DL.csv $(SUMMARIES_DIR)/tensorflow-all.csv $(SUMMARIES_DIR)/tensorflow-selected.csv $(SUMMARIES_DIR)/lazar-all.csv $(SUMMARIES_DIR)/lazar-high-confidence.csv $(SUMMARIES_DIR)/lazar-padel-all.csv $(SUMMARIES_DIR)/lazar-padel-high-confidence.csv
+
+CONFUSION_MATRICES = $(CONFUSION_MATRICES_DIR)/R-SVM.csv $(CONFUSION_MATRICES_DIR)/R-RF.csv $(CONFUSION_MATRICES_DIR)/R-DL.csv $(CONFUSION_MATRICES_DIR)/tensorflow-all.csv $(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv $(CONFUSION_MATRICES_DIR)/lazar-all.csv $(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-all.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-high-confidence.csv
 
 DATA = data/mutagenicity.sdf data/mutagenicity.csv data/mutagenicity-fingerprints.csv
 
 all: $(SUMMARIES) $(DATA) #$(tables)
+export: $(DATA) 
 
 # summaries
 
@@ -57,35 +64,33 @@ $(CONFUSION_MATRICES_DIR)/R-DL.csv: $(R_CV_DIR)/Sgl-Observations-DL.csv
 	scripts/cv-r-confusion-matrix.rb $< > $@
 
 ## lazar
-$(CONFUSION_MATRICES_DIR)/lazar-all.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
-	scripts/cv-lazar-confusion-matrix.rb all $< > $@
+$(CONFUSION_MATRICES_DIR)/lazar-all.csv: $(LAZAR_CONFUSION_MATRIX_DIR)
+	cp $</all $@
+
+$(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv: $(LAZAR_CONFUSION_MATRIX_DIR)
+	cp $</high_confidence $@
 
-$(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
-	scripts/cv-lazar-confusion-matrix.rb high-confidence $< > $@
+$(CONFUSION_MATRICES_DIR)/lazar-padel-all.csv: $(LAZAR_PADEL_CONFUSION_MATRIX_DIR)
+	cp $</all $@
 
-# TODO lazar model/cv with PaDEL descriptors
+$(CONFUSION_MATRICES_DIR)/lazar-padel-high-confidence.csv: $(LAZAR_PADEL_CONFUSION_MATRIX_DIR)
+	cp $</high_confidence $@
 
 # exports
 
-data/mutagenicity-fingerprints.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
-	scripts/export-fingerprints.rb $< > $@
+data/mutagenicity-fingerprints.csv: $(LAZAR_DIR)/models/mutagenicity
+	$(LAZAR_DIR)/bin/export-fingerprints.rb $< > $@
 
-data/mutagenicity.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
-	scripts/export.rb $< training_csv > $@
+data/mutagenicity.csv: $(LAZAR_DIR)/models/mutagenicity/Mutagenicity-Salmonella_typhimurium.csv
+	cp $< > $@
 
-data/mutagenicity.sdf: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
-	scripts/export.rb $< sdf > $@
+data/mutagenicity.sdf: $(LAZAR_DIR)/models/mutagenicity/Mutagenicity-Salmonella_typhimurium.csv
+	$(LAZAR_DIR)/bin/export-sdf.rb $< > $@
 	
 # lazar models and crossvalidations
 
+$(LAZAR_SUMMARY_DIR):
+	make -C $(LAZAR_MODEL_DIR)
 
-$(LAZAR_CV_DIR)/lazar-crossvalidation.id: ../lazar/data/Mutagenicity-Salmonella_typhimurium.csv # adjust to match the location of your lazar libraries
-	scripts/lazar-crossvalidation.rb $< > $@
-
-# import
-# TODO lazar model/cv with PaDEL descriptors
-
-# cleanup
-
-drop-database:
-	scripts/drop-database.rb
+$(LAZAR_PADEL_SUMMARY_DIR):
+	make -C $(LAZAR_PADEL_MODEL_DIR)
-- 
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