fingerprint predictions addedsingle-input-file

1 files changed, 4 insertions, 30 deletions

diff --git a/models/mutagenicity-mp2d/Makefile b/models/mutagenicity-mp2d/Makefile
index b80be6d..7e870b1 100644
--- a/models/mutagenicity-mp2d/Makefile
+++ b/models/mutagenicity-mp2d/Makefile
@@ -1,49 +1,23 @@
-SRC = Mutagenicity-Salmonella_typhimurium.csv 
 LAZAR_BIN = ../../bin
-MODEL = independent-variable-type dependent-variable-type dependent-variable-values similarity-thresholds independent-variables dependent-variables smiles metadata.json
 
-all: crossvalidation/summaries
-
-model: $(MODEL)
+all: crossvalidation/summary-all.csv metadata.json
 
 # Crossvalidation
 
-crossvalidation/summaries: crossvalidation
-	$(LAZAR_BIN)/classification-summary.rb crossvalidation
-
-crossvalidation: $(MODEL)
-	$(LAZAR_BIN)/crossvalidation.rb .
+crossvalidation/summary-all.csv: mutagenicity.csv
+	$(LAZAR_BIN)/lazar -t $< -x
 
 # Model
 
+# TODO fingerprint generation
 independent-variables: smiles
 	$(LAZAR_BIN)/fingerprints.rb smiles > $@
 
-dependent-variables: $(SRC)
-	cut -f2 -d ',' $< | sed '1d' > $@
-
-smiles: $(SRC)
-	cut -f1 -d ',' $< | sed '1d' > $@
-
 # 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" > $@
-
-dependent-variable-type:
-	echo "binary" > $@
-
-dependent-variable-values:
-	echo -e "\"0\"\n\"1\"" > $@
-
-similarity-thresholds:
-	echo -e "0.2\n0.5" > $@
-
 # Merge data
 
 Mutagenicity-Salmonella_typhimurium.csv: download/efsa.csv download/hansen.csv download/kazius.csv