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# Manuscript
# Requirements:
# pandoc-scholar (https://github.com/pandoc-scholar/pandoc-scholar) in PANDOC_SCHOLAR_PATH
# pandoc-placetable (https://github.com/mb21/pandoc-placetable)
# manuscript
ARTICLE_FILE = mutagenicity.mustache.md
PANDOC_SCHOLAR_PATH = pandoc-scholar
OUTFILE_PREFIX = mutagenicity
DEFAULT_EXTENSIONS = pdf
PANDOC_WRITER_OPTIONS = --filter=pandoc-placetable --filter=pandoc-crossref --filter=pandoc-citeproc
TEMPLATE_FILE_LATEX = pandoc-scholar.latex
# experiments
# crossvalidations
CV_DIR = 10-fold-crossvalidations/
LAZAR_MP2D_CONFUSION_MATRIX_DIR = $(CV_DIR)mp2d/lazar/crossvalidation/confusion_matrices/
LAZAR_CDK_CONFUSION_MATRIX_DIR = $(CV_DIR)cdk/lazar/crossvalidation/confusion_matrices/
TENSORFLOW_MP2D_CV_DIR = $(CV_DIR)mp2d/tensorflow/
TENSORFLOW_CDK_CV_DIR = $(CV_DIR)cdk/tensorflow/
CONFUSION_MATRICES_DIR = $(CV_DIR)confusion-matrices/
LAZAR_CONFUSION_MATRICES = $(addprefix $(CONFUSION_MATRICES_DIR), \
lazar-mp2d-all.csv \
lazar-mp2d-high-confidence.csv \
lazar-cdk-all.csv \
lazar-cdk-high-confidence.csv \
)
TENSORFLOW_MP2D_CONFUSION_MATRICES = \
tensorflow-rf-mp2d.csv \
tensorflow-lr-mp2d.csv \
tensorflow-lr2-mp2d.csv \
tensorflow-nn-mp2d.csv \
tensorflow-svm-mp2d.csv
TENSORFLOW_CDK_CONFUSION_MATRICES = \
tensorflow-rf-cdk.csv \
tensorflow-lr-cdk.csv \
tensorflow-lr2-cdk.csv \
tensorflow-nn-cdk.csv \
tensorflow-svm-cdk.csv
TENSORFLOW_CONFUSION_MATRICES = $(addprefix $(CONFUSION_MATRICES_DIR), $(TENSORFLOW_MP2D_CONFUSION_MATRICES) $(TENSORFLOW_CDK_CONFUSION_MATRICES))
CONFUSION_MATRICES = $(LAZAR_CONFUSION_MATRICES) $(TENSORFLOW_CONFUSION_MATRICES)
CV_SUMMARY = $(CV_DIR)summary.yaml
# PA predictions
PA_DIR = pyrrolizidine-alkaloids/
PA_DATA_DIR = data/pyrrolizidine-alkaloids/
PA_MP2D_DIR = $(PA_DIR)mp2d/
PA_CDK_DIR = $(PA_DIR)cdk/
PA_MP2D_LAZAR_DIR = $(PA_MP2D_DIR)lazar/
PA_CDK_LAZAR_DIR = $(PA_CDK_DIR)lazar/
PA_MP2D_TENSORFLOW_DIR = $(PA_MP2D_DIR)tensorflow/
PA_CDK_TENSORFLOW_DIR = $(PA_CDK_DIR)tensorflow/
PA_MP2D_TENSORFLOW_PREDICTIONS = $(addprefix $(PA_MP2D_TENSORFLOW_DIR), \
pred.lr2.v5-ext-ext-Padel-2D.csv \
pred.lr.v5-ext-ext-Padel-2D.csv \
pred.nn.v5-ext-ext-Padel-2D.csv \
pred.rf.v5-ext-ext-Padel-2D.csv \
pred.svm.v5-ext-ext-Padel-2D.csv \
)
PA_CDK_TENSORFLOW_PREDICTIONS = $(addprefix $(PA_CDK_TENSORFLOW_DIR), \
pred.lr2.v5-ext-Padel-2D.csv \
pred.lr.v5-ext-Padel-2D.csv \
pred.nn.v5-ext-Padel-2D.csv \
pred.rf.v5-ext-Padel-2D.csv \
pred.svm.v5-ext-Padel-2D.csv \
)
PA_PREDICTIONS = \
$(PA_MP2D_LAZAR_DIR)pa-mp2d-predictions.csv \
$(PA_CDK_LAZAR_DIR)pa-cdk-predictions.csv \
$(PA_MP2D_TENSORFLOW_PREDICTIONS) \
$(PA_CDK_TENSORFLOW_PREDICTIONS)
PA_SUMMARY = $(PA_DIR)summary.yaml
# manuscript
TABLES = $(addprefix tables/, \
lazar-summary.csv \
tensorflow-summary.csv \
pa-tab.tex \
pa-summary.csv \
)
FIGURES = $(addprefix figures/, \
roc.png \
tsne-mp2d.png \
tsne-cdk.png \
Dehydropyrrolizidine.png \
Diester.png \
Macrocyclic.diester.png \
Monoester.png \
N.oxide.png \
Otonecine.png \
Platynecine.png \
Retronecine.png \
Tertiary.PA.png \
)
SUMMARY = summary.yaml
all: mutagenicity.pdf
include $(PANDOC_SCHOLAR_PATH)/Makefile
mutagenicity.mustache.md: mutagenicity.md $(TABLES) $(FIGURES) $(SUMMARY)
mustache $^ > $@
# figures
figures/tsne-cdk.png: figures/tsne-cdk.csv
scripts/tsne-cdk.R
# TODO: filtered CDK descriptors
figures/tsne-cdk.csv: data/training/GenoTox-database.csv data/pyrrolizidine-alkaloids/PA-Padel-2D_m2.csv
scripts/cdk-descriptors.rb $^ > $@
figures/tsne-mp2d.png: figures/tsne-mp2d.csv
scripts/tsne-mp2d.R
# TODO: exported fingerprints
figures/tsne-mp2d.csv: 10-fold-crossvalidations/mp2d/lazar/independent_variables
scripts/mp2d-distances.rb > figures/tsne-mp2d.csv
figures/roc.png: figures/roc.csv
scripts/roc.R
figures/roc.csv: $(CV_SUMMARY)
scripts/summary2roc.rb $< > $@
# tables
tables/pa-summary.csv: $(PA_SUMMARY)
scripts/pa-summary-table.rb $< > $@
tables/pa-tab.tex: tables/pa-table.csv
scripts/pa-tex-table.rb $< > $@
tables/pa-table.csv: $(PA_PREDICTIONS)
scripts/pa-table.rb > $@
tables/lazar-summary.csv: $(CV_SUMMARY)
scripts/summary2table.rb lazar > $@
tables/tensorflow-summary.csv: $(CV_SUMMARY)
scripts/summary2table.rb tensorflow > $@
$(SUMMARY): $(PA_SUMMARY) $(CV_SUMMARY)
scripts/summary.rb $^ > $@
# PA summary
$(PA_SUMMARY): tables/pa-table.csv
scripts/pa-summary.rb $< > $@
# PA lazar predictions
# TODO move to script dir, generate independent_variables from data
$(PA_CDK_LAZAR_DIR)pa-cdk-predictions.csv: $(PA_CDK_LAZAR_DIR)pa_independent_variables
../lazar/bin/batch_padel_classification.rb 10-fold-crossvalidations/lazar-pa-cdk $< > $@
$(PA_MP2D_LAZAR_DIR)pa-mp2d-predictions.csv: $(PA_DATA_DIR)pa-smiles.csv
../lazar/bin/batch_fingerprint_classification.rb ../lazar/models/mutagenicity $< > $@
$(PA_DATA_DIR)pa-smiles.csv: $(PA_DATA_DIR)180920_PA_complete_SMILES.csv
cut -f1,4 -d ';' $< | sed 's/;/,/' > $@
# crossvalidation summary
$(CV_SUMMARY): $(CONFUSION_MATRICES)
scripts/confusion-matrix-summary.rb $^ > $@
# confusion matrices
## lazar
$(CONFUSION_MATRICES_DIR)lazar-mp2d-all.csv: $(LAZAR_MP2D_CONFUSION_MATRIX_DIR)all
cp $< $@
$(CONFUSION_MATRICES_DIR)lazar-mp2d-high-confidence.csv: $(LAZAR_MP2D_CONFUSION_MATRIX_DIR)high_confidence
cp $< $@
$(CONFUSION_MATRICES_DIR)lazar-cdk-all.csv: $(LAZAR_CDK_CONFUSION_MATRIX_DIR)all
cp $< $@
$(CONFUSION_MATRICES_DIR)lazar-cdk-high-confidence.csv: $(LAZAR_CDK_CONFUSION_MATRIX_DIR)high_confidence
cp $< $@
## tensorflow
### mp2d
$(CONFUSION_MATRICES_DIR)tensorflow-lr-mp2d.csv: $(TENSORFLOW_MP2D_CV_DIR)pred.lr.v4_ext.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
$(CONFUSION_MATRICES_DIR)tensorflow-lr2-mp2d.csv: $(TENSORFLOW_MP2D_CV_DIR)pred.lr2.v4_ext.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
$(CONFUSION_MATRICES_DIR)tensorflow-nn-mp2d.csv: $(TENSORFLOW_MP2D_CV_DIR)pred.nn.v4_ext.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
$(CONFUSION_MATRICES_DIR)tensorflow-rf-mp2d.csv: $(TENSORFLOW_MP2D_CV_DIR)pred.rf.v4_ext.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
$(CONFUSION_MATRICES_DIR)tensorflow-svm-mp2d.csv: $(TENSORFLOW_MP2D_CV_DIR)pred.svm.v4_ext.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
### cdk
$(CONFUSION_MATRICES_DIR)tensorflow-lr-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.lr.v4.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
$(CONFUSION_MATRICES_DIR)tensorflow-lr2-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.lr2.v4.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
$(CONFUSION_MATRICES_DIR)tensorflow-nn-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.nn.v4.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
$(CONFUSION_MATRICES_DIR)tensorflow-rf-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.rf.v4.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
$(CONFUSION_MATRICES_DIR)tensorflow-svm-cdk.csv: $(TENSORFLOW_CDK_CV_DIR)pred.svm.v4.csv
scripts/cv-tensorflow-confusion-matrix.rb $< > $@
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