diff options
Diffstat (limited to 'Makefile')
-rw-r--r-- | Makefile | 71 |
1 files changed, 30 insertions, 41 deletions
@@ -1,81 +1,67 @@ -data = data/kazius.csv data/efsa.csv data/hansen.csv +summaries = summaries/mutagenicity-merged-crossvalidations.json summaries/carcinogenicity-crossvalidations.json summaries/pa_mutagenicity_neighbor_sets.json summaries/pa_carcinogenicity_neighbor_sets.json -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 +exports = export/mutagenicity-merged.sdf export/pa_mutagenicity.csv export/pa_carcinogenicity.csv -all: $(summaries) +all: $(summaries) $(exports) -# exports - -export/mutagenicity-merged.sdf: data/mutagenicity-merged.id - scripts/export.rb $< sdf > $@ - -export/mutagenicity-merged.csv: data/mutagenicity-merged.id - scripts/export.rb $< > $@ - -export/carcinogenicity.csv: data/carcinogenicity.id - scripts/export.rb $< > $@ +# summaries -summaries/pa_carcinogenicity_neighbor_sets.json: experiments/pa_carcinogenicity_prediction.json +summaries/pa_carcinogenicity_neighbor_sets.json: data/pa_carcinogenicity.json scripts/pa_neighbor_sets.rb $< > $@ -summaries/pa_mutagenicity_neighbor_sets.json: experiments/pa_mutagenicity_prediction.json +summaries/pa_mutagenicity_neighbor_sets.json: data/pa_mutagenicity.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 $< > $@ +summaries/mutagenicity-merged-crossvalidations.json: models/mutagenicity-merged.id + scripts/crossvalidation-summary.rb $< > $@ -experiments/weighted_majority_kazius_sim0.5.id: data/kazius.csv - scripts/repeated_crossvalidation.rb $< > $@ +summaries/carcinogenicity-crossvalidations.json: models/carcinogenicity.id + scripts/crossvalidation-summary.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/mutagenicity-merged.csv - scripts/repeated_crossvalidation.rb $< > $@ +# exports -summaries/weighted_majority_kazius_sim0.1.json: experiments/weighted_majority_kazius_sim0.1.id - scripts/repeated_crossvalidation_summary.rb $< > $@ +export/mutagenicity-merged.sdf: data/mutagenicity-merged.id + scripts/export.rb $< > $@ -experiments/weighted_majority_kazius_sim0.1.id: data/kazius.csv - scripts/repeated_crossvalidation.rb $< > $@ +export/pa_mutagenicity.csv: data/pa_mutagenicity.json + scripts/json2csv.rb $< > $@ -summaries/weighted_majority_merged_sim0.1.json: experiments/weighted_majority_merged_sim0.1.id - scripts/repeated_crossvalidation_summary.rb $< > $@ +export/pa_carcinogenicity.csv: data/pa_carcinogenicity.json + scripts/json2csv.rb $< > $@ -experiments/weighted_majority_merged_sim0.1.id: data/mutagenicity-merged.csv - scripts/repeated_crossvalidation.rb $< > $@ +# predictions -experiments/pa_carcinogenicity.id: data/carcinogenicity.id data/PA.id +data/pa_carcinogenicity.json: models/carcinogenicity.id data/PA.id scripts/predict.rb $^ > $@ -experiments/pa_mutagenicity.id: data/mutagenicity-merged.id data/PA.id +data/pa_mutagenicity.json: models/mutagenicity-merged.id data/PA.id scripts/predict.rb $^ > $@ -# models +# models and validations models/mutagenicity-merged.id: data/mutagenicity-merged.id - scripts/merge.rb $^ > $@ + scripts/model.rb $< > $@ models/carcinogenicity.id: data/carcinogenicity.id - scripts/import-pubchem.rb 1205 + scripts/model.rb $< > $@ # test data data/PA.id: data/PA.sdf - scripts/import.rb $< sdf > $@ + scripts/import.rb $< > $@ # training data -data/mutagenicity-merged.id: data/hansen.id data/kazius.id data/efsa.id +data/mutagenicity-merged.id: data/hansen.id data/efsa.id data/kazius.id scripts/merge.rb $^ > $@ data/carcinogenicity.id: - scripts/import-pubchem.rb 1205 + scripts/import-pubchem.rb 1205 > $@ # kazius data/kazius.id: data/cas_4337.sdf - scripts/import.rb $< sdf > $@ + scripts/import.rb $< > $@ data/cas_4337.sdf: data/cas_4337.zip cd data && unzip cas_4337.zip @@ -113,5 +99,8 @@ data/Mutagenicity_N6512.csv: clean: rm data/*.id +clean_db: + rm data/*.id && scripts/drop-database.rb + cleanall: rm data/* |