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# Manuscript
# please install pandoc-scholar (https://github.com/pandoc-scholar/pandoc-scholar) in the pandoc-scholar directory or point PANDOC_SCHOLAR_PATH to tour installation
ARTICLE_FILE = mutagenicity.md
PANDOC_SCHOLAR_PATH = pandoc-scholar
OUTFILE_PREFIX = mutagenicity
DEFAULT_EXTENSIONS = latex pdf docx #odt epub html
PANDOC_WRITER_OPTIONS = --filter=pandoc-citeproc
#PANDOC_WRITER_OPTIONS = --filter=pandoc-placetable --filter=pandoc-citeproc
TEMPLATE_FILE_LATEX = pandoc-scholar.latex
include $(PANDOC_SCHOLAR_PATH)/Makefile
# Lazar
LAZAR_DIR = "../lazar"
# Experiments
SUMMARIES_DIR = 10-fold-crossvalidations/summaries
CONFUSION_MATRICES_DIR = 10-fold-crossvalidations/confusion-matrices
R_CV_DIR = 10-fold-crossvalidations/R
TENSORFLOW_CV_DIR = 10-fold-crossvalidations/tensorflow
LAZAR_CV_DIR = 10-fold-crossvalidations/lazar
#tables = tables/R-SVM.csv tables/R-RF.csv tables/R-DL.csv
SUMMARIES = $(SUMMARIES_DIR)/R-SVM.csv $(SUMMARIES_DIR)/R-RF.csv $(SUMMARIES_DIR)/R-DL.csv $(SUMMARIES_DIR)/tensorflow-all.csv $(SUMMARIES_DIR)/tensorflow-selected.csv $(SUMMARIES_DIR)/lazar-all.csv $(SUMMARIES_DIR)/lazar-high-confidence.csv
# TODO lazar model/cv with PaDEL descriptors
DATA = data/mutagenicity.sdf data/mutagenicity.csv data/mutagenicity-fingerprints.csv
all: $(SUMMARIES) $(DATA) #$(tables)
# summaries
$(SUMMARIES_DIR)/%.csv: $(CONFUSION_MATRICES_DIR)/%.csv
scripts/confusion-matrix-summary.rb $< > $@
# confusion matrices
## tensorflow
$(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv: $(TENSORFLOW_CV_DIR)/pred.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
$(CONFUSION_MATRICES_DIR)/tensorflow-all.csv: $(TENSORFLOW_CV_DIR)/pred_ext.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
## R
$(CONFUSION_MATRICES_DIR)/R-SVM.csv: $(R_CV_DIR)/Sgl-Observations-SVM.csv
scripts/cv-r-confusion-matrix.rb $< > $@
$(CONFUSION_MATRICES_DIR)/R-RF.csv: $(R_CV_DIR)/Sgl-Observations-RF.csv
scripts/cv-r-confusion-matrix.rb $< > $@
$(CONFUSION_MATRICES_DIR)/R-DL.csv: $(R_CV_DIR)/Sgl-Observations-DL.csv
scripts/cv-r-confusion-matrix.rb $< > $@
## lazar
$(CONFUSION_MATRICES_DIR)/lazar-all.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
scripts/cv-lazar-confusion-matrix.rb all $< > $@
$(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
scripts/cv-lazar-confusion-matrix.rb high-confidence $< > $@
# TODO lazar model/cv with PaDEL descriptors
# exports
data/mutagenicity-fingerprints.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
scripts/export-fingerprints.rb $< > $@
data/mutagenicity.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
scripts/export.rb $< training_csv > $@
data/mutagenicity.sdf: $(LAZAR_CV_DIR)/lazar-crossvalidation.id
scripts/export.rb $< sdf > $@
# lazar models and crossvalidations
$(LAZAR_CV_DIR)/lazar-crossvalidation.id: ../lazar/data/Mutagenicity-Salmonella_typhimurium.csv # adjust to match the location of your lazar libraries
scripts/lazar-crossvalidation.rb $< > $@
# import
# TODO lazar model/cv with PaDEL descriptors
# cleanup
drop-database:
scripts/drop-database.rb
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