Makefile

MAKEFLAGS 				+= --warn-undefined-variables
SHELL 					:= bash
.DEFAULT_GOAL			:= help
URIBASE					:=	http://purl.obolibrary.org/obo
TMP_DATA				:=	data/tmp

ROOT_DIR				:=	$(shell pwd)

PHENOTYPE_DIR			:= $(ROOT_DIR)/data/phenotype
RUNNERS_DIR				:= $(ROOT_DIR)/runners
NAME					:= $(shell python -c 'import tomli; print(tomli.load(open("pyproject.toml", "rb"))["tool"]["poetry"]["name"])')
VERSION					:= $(shell python -c 'import tomli; print(tomli.load(open("pyproject.toml", "rb"))["tool"]["poetry"]["version"])')
SEMSIM_BASE_URL			:= https://storage.googleapis.com/data-public-monarchinitiative/semantic-similarity/latest



help: info
	@echo ""
	@echo "help"
	@echo "make setup -- this runs the download and extraction of genomic, phenotypic and runners data"
	@echo "make pheval -- this runs pheval pipeline corpus preparation and run"
	@echo "make all -- this runs the entire pipeline including setup, corpus preparation and pheval run"
	@echo "make help -- show this help"
	@echo ""

info:
	@echo "Project: $(NAME)"
	@echo "Version: $(VERSION)"

.PHONY: prepare-inputs






configurations/template-1.0.0/config.yaml:
	mkdir -p $(ROOT_DIR)/$(shell dirname $@)/
	cp $(RUNNERS_DIR)/configurations/template-1.0.0.config.yaml $(ROOT_DIR)/$(shell dirname $@)/config.yaml







.PHONY: prepare-corpora


$(TMP_DATA)/semsim/%.tsv:
	mkdir -p $(TMP_DATA)/semsim/
	wget $(SEMSIM_BASE_URL)/$*.tsv -O $@


$(TMP_DATA)/semsim/%.sql:
	mkdir -p $(TMP_DATA)/semsim/
	wget $(SEMSIM_BASE_URL)/$*.sql -O $@




$(ROOT_DIR)/results/template-1.0.0/results.yml: configurations/template-1.0.0/config.yaml corpora/lirical/default/corpus.yml



	rm -rf $(ROOT_DIR)/$(shell dirname $@)
	mkdir -p $(ROOT_DIR)/$(shell dirname $@)



	mkdir -p $(shell dirname $@)

	pheval run \
	 --input-dir $(ROOT_DIR)/configurations/template-1.0.0 \
	 --testdata-dir $(ROOT_DIR)/corpora/lirical/default \
	 --runner templatephevalrunner \
	 --tmp-dir data/tmp/ \
	 --version 1.0.0 \
	 --output-dir $(shell dirname $@)

	touch $@

.PHONY: pheval-run
pheval-run: $(ROOT_DIR)/results/template-1.0.0/results.yml


$(ROOT_DIR)/results/template-1.0.0/run_data.yaml:
	printf '%s\n' \
	"benchmark_name: fake_predictor_benchmark" \
	"runs:" \
	"  - run_identifier: run_identifier_1" \
	"    results_dir: $(shell dirname $@)" \
	"    phenopacket_dir: $(ROOT_DIR)/corpora/lirical/default/phenopackets" \
	"    gene_analysis: True" \
	"    variant_analysis: False" \
	"    disease_analysis: False" \
	"    threshold:" \
	"    score_order: descending" \
	"plot_customisation:" \
	"  gene_plots:" \
	"    plot_type: bar_cumulative" \
	"    rank_plot_title:" \
	"    roc_curve_title: " \
	"    precision_recall_title: " \
	"  disease_plots:" \
	"    plot_type: bar_cumulative" \
	"    rank_plot_title:" \
	"    roc_curve_title: " \
	"    precision_recall_title: " \
	"  variant_plots:" \
	"    plot_type: bar_cumulative" \
	"    rank_plot_title: " \
	"    roc_curve_title: " \
	"    precision_recall_title: " \
	> $@

$(ROOT_DIR)/results/template-1.0.0/gene_rank_stats.svg: $(ROOT_DIR)/results/template-1.0.0/run_data.yaml
	pheval-utils generate-benchmark-stats -r $<

.PHONY: pheval-report
pheval-report: $(ROOT_DIR)/results/template-1.0.0/gene_rank_stats.svg


corpora/lirical/default/corpus.yml:
	test -d $(ROOT_DIR)/corpora/lirical/default/ || mkdir -p $(ROOT_DIR)/corpora/lirical/default/

	test -L $(ROOT_DIR)/corpora/lirical/default/template_exome_hg19.vcf.gz || ln -s $(ROOT_DIR)/testdata/template_vcf/template_exome_hg19.vcf.gz $(ROOT_DIR)/corpora/lirical/default/template_exome_hg19.vcf.gz
	pheval-utils create-spiked-vcfs \
	 --hg19-template-vcf $(ROOT_DIR)/corpora/lirical/default/template_exome_hg19.vcf.gz  \
	 --phenopacket-dir=$(ROOT_DIR)/corpora/lirical/default/phenopackets \
	 --output-dir $(ROOT_DIR)/corpora/lirical/default/vcf
	touch $@



.PHONY: pheval
pheval:
	$(MAKE) prepare-inputs
	$(MAKE) prepare-corpora
	$(MAKE) pheval-run
	$(MAKE) pheval-report

.PHONY: all
all:
	$(MAKE) setup
	$(MAKE) pheval

include ./resources/custom.Makefile