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# Manuscript
# Requirements:
# pandoc-scholar (https://github.com/pandoc-scholar/pandoc-scholar) in PANDOC_SCHOLAR_PATH
# manuscript
ARTICLE_FILE = mutagenicity.mustache.md
PANDOC_SCHOLAR_PATH = pandoc-scholar
OUTFILE_PREFIX = mutagenicity
DEFAULT_EXTENSIONS = pdf
PANDOC_WRITER_OPTIONS = --filter=pandoc-crossref --filter=pandoc-citeproc
TEMPLATE_FILE_LATEX = pandoc-scholar.latex
# experiments
# crossvalidations
CV_DIR = crossvalidations/
CV_PREDICTIONS_DIR = $(CV_DIR)predictions/
LAZAR_MODELS_DIR = ../lazar/models/
LAZAR_PREDICTIONS_DIR = ../lazar/predictions/
TENSORFLOW_CV_DIR = $(CV_DIR)/tensorflow/
CONFUSION_MATRICES_DIR = $(CV_DIR)confusion-matrices/
CV_FILES = lazar-all.csv lazar-high-confidence.csv rf.csv lr.csv lr2.csv nn.csv svm.csv
CONFUSION_MATRICES = $(addprefix $(CONFUSION_MATRICES_DIR)mp2d/, $(CV_FILES)) $(addprefix $(CONFUSION_MATRICES_DIR)cdk/, $(CV_FILES))
CV_PREDICTIONS = $(addprefix $(CV_PREDICTIONS_DIR)mp2d/, $(CV_FILES)) $(addprefix $(CV_PREDICTIONS_DIR)cdk/, $(CV_FILES))
CV_SUMMARY = $(CV_DIR)summary.yaml
# PA predictions
PA_DIR = pyrrolizidine-alkaloids/
TENSORFLOW_PA_DIR = $(PA_DIR)tensorflow/
PA_MP2D_LAZAR_DIR = $(PA_MP2D_DIR)lazar/
PA_CDK_LAZAR_DIR = $(PA_CDK_DIR)lazar/
PA_PREDICTIONS = $(addprefix $(PA_DIR)mp2d/, $(CV_FILES)) $(addprefix $(PA_DIR)cdk/, $(CV_FILES))
PA_SUMMARY = $(PA_DIR)summary.yaml
# manuscript
PA_FIGURES = $(addprefix figures/, \
Dehydropyrrolizidine.png \
Diester.png \
Macrocyclic.diester.png \
Monoester.png \
N.oxide.png \
Otonecine.png \
Platynecine.png \
Retronecine.png \
Tertiary.PA.png \
)
FIGURES = figures/roc.png figures/tsne-mp2d-mutagenicity.png figures/tsne-cdk-mutagenicity.png $(PA_FIGURES)
DATA = data.yaml
all: mutagenicity.pdf $(PA_DIR)pa-predictions.pdf $(CV_PREDICTIONS) $(CONFUSION_MATRICES) $(PA_PREDICTIONS)
include $(PANDOC_SCHOLAR_PATH)/Makefile
mutagenicity.mustache.md: $(DATA) mutagenicity.md $(FIGURES)
mustache $^ > $@
# manuscript data
$(DATA): $(PA_SUMMARY) $(CV_SUMMARY) mutagenicity/mutagenicity.csv mutagenicity/mutagenicity-cdk.csv $(PA_DIR)pa-predictions.csv
scripts/data.rb $^ > $@
# figures
## tsne
figures/tsne-%-mutagenicity.png: figures/tsne-%-coordinates.csv figures/tsne-%-mutagenicity.csv
Rscript scripts/tsne-mutagenicity.R $^ $@
### factors
figures/tsne-%-mutagenicity.csv: figures/tsne-%-coordinates.csv mutagenicity/mutagenicity.csv
scripts/tsne-mutagenicity.rb $^ > $@
### coordinates
figures/tsne-cdk-coordinates.csv: figures/tsne-cdk-descriptors.csv
Rscript scripts/tsne-cdk-coordinates.R $< $@
figures/tsne-mp2d-coordinates.csv: figures/tsne-mp2d-distances.csv
Rscript scripts/tsne-mp2d-coordinates.R $< $@
### input
figures/tsne-cdk-descriptors.csv: mutagenicity/mutagenicity-cdk.csv pyrrolizidine-alkaloids/pa-cdk.csv
scripts/tsne-cdk-descriptors.rb $^ > $@
figures/tsne-mp2d-distances.csv: mutagenicity/mutagenicity-mp2d pyrrolizidine-alkaloids/pa-mp2d
scripts/tsne-mp2d-distances.rb $^ > $@
## roc
figures/roc.png: figures/roc.csv
Rscript scripts/roc.R
figures/roc.csv: $(CV_SUMMARY)
scripts/roc.rb $< > $@
## pa predictions per group
$(PA_FIGURES): $(PA_DIR)pa-groups.csv $(PA_DIR)pa-predictions.csv
scripts/pa-groups.R $^
# PA predictions
## summary
$(PA_SUMMARY): $(PA_DIR)pa-predictions.csv
scripts/pa-summary.rb $< > $@
## pdf table
$(PA_DIR)pa-predictions.pdf: $(PA_DIR)pa-predictions.tex
pdflatex -output-directory $(PA_DIR) $(PA_DIR)pa-predictions.tex
$(PA_DIR)pa-predictions.tex: $(PA_DIR)/pa-groups.csv $(PA_DIR)pa-predictions.csv
scripts/pa-predictions-latex.rb $^ > $@
## table
$(PA_DIR)pa-predictions.csv: $(PA_PREDICTIONS)
scripts/pa-predictions.rb $^ > $@
## predictions
$(PA_DIR)%/lazar-all.csv: $(LAZAR_PREDICTIONS_DIR)pa-%/predictions
scripts/lazar-pa-predictions.rb $< > $@
$(PA_DIR)%/lazar-high-confidence.csv: $(LAZAR_PREDICTIONS_DIR)pa-%/predictions
scripts/lazar-pa-predictions.rb $< 0.5 > $@
$(PA_DIR)mp2d/%.csv: $(TENSORFLOW_PA_DIR)pred.%.v5-ext-ext-Padel-2D.csv $(PA_DIR)pa-cids.csv
scripts/tensorflow-pa-predictions.rb $^ > $@
$(PA_DIR)cdk/%.csv: $(TENSORFLOW_PA_DIR)pred.%.v5-ext-Padel-2D.csv $(PA_DIR)pa-cids.csv
scripts/tensorflow-pa-predictions.rb $^ > $@
## sanitize PA input data
$(PA_DIR)pa-ids.csv $(PA_DIR)pa-cids.csv $(PA_DIR)pa-names.tsv $(PA_DIR)pa-groups.csv $(PA_DIR)pa-cdk.csv: $(PA_DIR)src/180920_PA_complete_SMILES.csv $(PA_DIR)src/pa-groups.original.csv $(PA_DIR)src/PA-Padel-2D_m2.csv
scripts/sanitize-pa-data.rb
# crossvalidation
## summary
$(CV_SUMMARY): $(CONFUSION_MATRICES)
scripts/cv-summary.rb $^ > $@
## confusion matrices
$(CONFUSION_MATRICES_DIR)%: $(CV_PREDICTIONS_DIR)%
scripts/confusion-matrix.rb $< > $@
## predictions
$(CV_PREDICTIONS_DIR)%/lazar-all.csv: $(LAZAR_MODELS_DIR)mutagenicity-%
scripts/lazar-cv-predictions.rb $< > $@
$(CV_PREDICTIONS_DIR)%/lazar-high-confidence.csv: $(LAZAR_MODELS_DIR)mutagenicity-%
scripts/lazar-cv-predictions.rb $< 0.5 > $@
$(CV_PREDICTIONS_DIR)mp2d/%.csv: $(TENSORFLOW_CV_DIR)pred.%.v4_ext.csv
scripts/tensorflow-cv-predictions.rb $< > $@
$(CV_PREDICTIONS_DIR)cdk/%.csv: $(TENSORFLOW_CV_DIR)pred.%.norm.v4.csv
scripts/tensorflow-cv-predictions.rb $< > $@
# cdk descriptors
mutagenicity/mutagenicity-cdk.csv: mutagenicity/src/mutagenicity-mod-2.new.csv
cut -f1,3- -d ',' $< > $@
# mp2d fingerprints
mutagenicity/mutagenicity-mp2d: mutagenicity/mutagenicity.csv
scripts/mp2d-fingerprints.rb $< > $@
$(PA_DIR)pa-mp2d: $(PA_DIR)pa-cids.csv
scripts/mp2d-fingerprints.rb $< > $@
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