From 791398c12af4f8290095425dac87e3c852905ab6 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Sat, 7 Sep 2019 18:20:10 +0200
Subject: obsolete data and java directories deleted

---
 models/mutagenicity/Makefile | 50 ++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 48 insertions(+), 2 deletions(-)

(limited to 'models/mutagenicity/Makefile')

diff --git a/models/mutagenicity/Makefile b/models/mutagenicity/Makefile
index 637004c..1e0c565 100644
--- a/models/mutagenicity/Makefile
+++ b/models/mutagenicity/Makefile
@@ -1,12 +1,28 @@
 LAZAR_BIN = ../../bin
-METADATA = independent_variable_type dependent_variable_type dependent_variable_values similarity_thresholds
+PARAMETERS = independent_variable_type dependent_variable_type dependent_variable_values similarity_thresholds
+
+all: crossvalidation/summaries metadata.json
+
+# Crossvalidation
+
+crossvalidation/summaries: crossvalidation
+	$(LAZAR_BIN)/classification_summary.rb crossvalidation
 
 crossvalidation: independent_variables
 	$(LAZAR_BIN)/classification_crossvalidation.rb .
 
-independent_variables: Mutagenicity-Salmonella_typhimurium.csv $(METADATA)
+# Model
+
+independent_variables: Mutagenicity-Salmonella_typhimurium.csv $(PARAMETERS)
 	$(LAZAR_BIN)/fingerprint_independent_variables.rb $< 
 
+# Metadata
+
+metadata.json:
+	echo '{"species":"Salmonella typhimurium","endpoint":"Mutagenicity","source":"http://cheminformatics.org/datasets/bursi/cas_4337.zip, http://doc.ml.tu-berlin.de/toxbenchmark/Mutagenicity_N6512.csv, https://data.europa.eu/euodp/data/storage/f/2017-07-19T142131/GENOTOX data and dictionary.xls","qmrf":{"group":"QMRF 4.10. Mutagenicity","name":"OECD 471 Bacterial Reverse Mutation Test"}}' > $@
+
+# Model parameters
+
 independent_variable_type:
 	echo "binary" > $@
 
@@ -18,3 +34,33 @@ dependent_variable_values:
 
 similarity_thresholds:
 	echo -e "0.2\n0.5" > $@
+
+# Merge data
+
+Mutagenicity-Salmonella_typhimurium.csv: download/efsa.csv download/hansen.csv download/kazius.csv
+	$(LAZAR_BIN)/merge_csv.rb $^
+
+# Convert data
+
+download/efsa.csv: download/efsa.tsv
+	download/efsa_classification.rb $< > $@
+
+download/efsa.tsv: download/efsa.xls
+	xls2csv -s cp1252 -d utf-8 -x -c "	" $< > $@
+
+download/hansen.csv: download/Mutagenicity_N6512.csv
+	download/hansen_convert.rb $< > $@
+
+download/kazius.csv: download/cas_4337.sdf
+	$(LAZAR_BIN)/sdf2csv.rb $< > $@
+
+# Download original data
+
+download/cas_4337.sdf:
+	cd download && wget http://cheminformatics.org/datasets/bursi/cas_4337.zip && unzip cas_4337.zip
+
+download/Mutagenicity_N6512.csv:
+	cd download && wget http://doc.ml.tu-berlin.de/toxbenchmark/Mutagenicity_N6512.csv
+
+download/efsa.xls:
+	wget "https://data.europa.eu/euodp/data/storage/f/2017-07-19T142131/GENOTOX data and dictionary.xls" -o $@
-- 
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