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# TODO
# efsa smiles errors (encodings?)
# efsa script via csv
# remove headers from csv files
# add header at merged csv
# remove \u003e/00
# remove log messages in result
data = data/kazius.csv data/efsa.csv data/hansen.csv
summaries = summaries/weighted_majority_merged_sim0.1.json summaries/weighted_majority_kazius_sim0.1.json summaries/weighted_majority_merged_sim0.5.json summaries/weighted_majority_kazius_sim0.5.json summaries/pa_mutagenicity_neighbor_sets.json summaries/pa_carcinogenicity_neighbor_sets.json
all: $(summaries)
summaries/pa_carcinogenicity_neighbor_sets.json: experiments/pa_carcinogenicity_prediction.json
scripts/pa_neighbor_sets.rb $< > $@
summaries/pa_mutagenicity_neighbor_sets.json: experiments/pa_mutagenicity_prediction.json
scripts/pa_neighbor_sets.rb $< > $@
summaries/weighted_majority_kazius_sim0.5.json: experiments/weighted_majority_kazius_sim0.5.id
scripts/repeated_crossvalidation_summary.rb $< > $@
experiments/weighted_majority_kazius_sim0.5.id: data/kazius.csv
scripts/repeated_crossvalidation.rb $< > $@
summaries/weighted_majority_merged_sim0.5.json: experiments/weighted_majority_merged_sim0.5.id
scripts/repeated_crossvalidation_summary.rb $< > $@
experiments/weighted_majority_merged_sim0.5.id: data/merged.csv
scripts/repeated_crossvalidation.rb $< > $@
summaries/weighted_majority_kazius_sim0.1.json: experiments/weighted_majority_kazius_sim0.1.id
scripts/repeated_crossvalidation_summary.rb $< > $@
experiments/weighted_majority_kazius_sim0.1.id: data/kazius.csv
scripts/repeated_crossvalidation.rb $< > $@
summaries/weighted_majority_merged_sim0.1.json: experiments/weighted_majority_merged_sim0.1.id
scripts/repeated_crossvalidation_summary.rb $< > $@
experiments/weighted_majority_merged_sim0.1.id: data/merged.csv
scripts/repeated_crossvalidation.rb $< > $@
experiments/pa_carcinogenicity_prediction.json: data/carcinogenicity.csv data/PA_complete_SMILES_fixed.csv
scripts/predict.rb $^ > $@
experiments/pa_mutagenicity_prediction.json: data/merged.csv data/PA_complete_SMILES_fixed.csv
scripts/predict.rb $^ > $@
# test data
data/PA_complete_SMILES_fixed.csv: data/PA_complete_SMILES.csv
cat $< | scripts/convert_pa.rb > $@
# training data
data/merged.csv: $(data)
echo "SMILES,Activity" > $@ && cat $(data) | sort -u | sed '/SMILES/d' >> $@
data/carcinogenicity.csv: data/aid1205.csv
scripts/carcinogenicity2csv.rb $< > $@
# carcinogenicity
data/aid1205.csv:
cd data && curl https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1205/CSV -o $@
# kazius
data/kazius.csv: data/cas_4337.sdf
scripts/kazius2csv.rb $< > $@
data/cas_4337.sdf: data/cas_4337.zip
cd data && unzip cas_4337.zip
data/cas_4337.zip:
cd data && wget "http://cheminformatics.org/datasets/bursi/cas_4337.zip"
# efsa
data/efsa.csv: data/GENOTOX_data_and_dictionary.csv
scripts/efsa2csv.rb $< > $@
data/GENOTOX_data_and_dictionary.csv: data/GENOTOX_data_and_dictionary.xls
xls2csv $< > $@
data/GENOTOX_data_and_dictionary.xls:
cd data && wget "https://data.europa.eu/euodp/data/storage/f/2017-07-19T142131/GENOTOX%20data%20and%20dictionary.xls" -o $@
# hansen
data/hansen.csv: data/Mutagenicity_N6512.csv
scripts/hansen2csv.rb $< > $@
data/Mutagenicity_N6512.csv:
cd data && wget "http://doc.ml.tu-berlin.de/toxbenchmark/Mutagenicity_N6512.csv"
clean:
rm data/hansen.csv
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