From a29eb3e38414cd252850c9c4fb356f8b2bef6fb4 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 12 Feb 2021 19:54:07 +0100 Subject: model.rb refactored, mp2d models updated --- models/mutagenicity/Makefile | 66 -------------------------------------------- 1 file changed, 66 deletions(-) delete mode 100644 models/mutagenicity/Makefile (limited to 'models/mutagenicity/Makefile') diff --git a/models/mutagenicity/Makefile b/models/mutagenicity/Makefile deleted file mode 100644 index 1e0c565..0000000 --- a/models/mutagenicity/Makefile +++ /dev/null @@ -1,66 +0,0 @@ -LAZAR_BIN = ../../bin -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 . - -# 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" > $@ - -dependent_variable_type: - echo "binary" > $@ - -dependent_variable_values: - echo -e "non-mutagenic\nmutagenic" > $@ - -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 $@ -- cgit v1.2.3