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-rw-r--r--models/mutagenicity/Makefile66
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diff --git a/models/mutagenicity/Makefile b/models/mutagenicity/Makefile
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--- a/models/mutagenicity/Makefile
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@@ -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 $@