EM_optimization/Makefile at master · zimmerlab/EM_optimization · GitHub

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PYTHON = biopython
DATA = /mnt/extproj/projekte/modelling/interactive_fuzzifier/FlowSets_selection

edges: specific_edges marker_edges
regulators: specific_regulators marker_regulators
targets: specific_targets marker_targets
.PHONY: edges, regulators, targets


specific_edges:	$(wildcard $(DATA)/miRNA/FV_raw_log2FC/final_fuzzy_values/*.tsv) \
				$(wildcard $(DATA)/RNA/FV_raw_log2FC/final_fuzzy_values/*.tsv) \
				sample_mapping.tsv \
				$(wildcard ./template_edges/*.tsv) \
				reference_edges.tsv \
				./config/EM_edges.json
	$(PYTHON) main_EM.py --input $(DATA)/miRNA/FV_raw_log2FC/final_fuzzy_values/ $(DATA)/RNA/FV_raw_log2FC/final_fuzzy_values/ \
		--metadata sample_mapping.tsv \
		--template ./template_edges/ \
		--reference reference_edges.tsv \
		--config ./config/EM_edges.json \
		--optimize_goal context-specific \
		--output ./output_edges/context-specific/


marker_edges:	$(wildcard $(DATA)/miRNA/FV_raw_log2FC/final_fuzzy_values/*.tsv) \
				$(wildcard $(DATA)/RNA/FV_raw_log2FC/final_fuzzy_values/*.tsv) \
				sample_mapping.tsv \
				$(wildcard ./template_edges/*.tsv) \
				reference_edges.tsv \
				./config/EM_edges.json
	$(PYTHON) main_EM.py --input $(DATA)/miRNA/FV_raw_log2FC/final_fuzzy_values/ $(DATA)/RNA/FV_raw_log2FC/final_fuzzy_values/ \
		--metadata sample_mapping.tsv \
		--template ./template_edges/ \
		--reference reference_edges.tsv \
		--config ./config/EM_edges.json \
		--optimize_goal marker \
		--output ./output_edges/markers/


specific_regulators:	$(wildcard $(DATA)/miRNA/FV_raw_log2FC/final_fuzzy_values/*.tsv) \
						sample_mapping.tsv \
						$(wildcard ./template_features/*.tsv) \
						./config/EM_regulators.json
	$(PYTHON) main_EM.py --input $(DATA)/miRNA/FV_raw_log2FC/final_fuzzy_values/ \
		--metadata sample_mapping.tsv \
		--template ./template_features/ \
		--config ./config/EM_regulators.json \
		--optimize_goal context-specific \
		--output ./output_regulators/context-specific/


marker_regulators:	$(wildcard $(DATA)/miRNA/FV_raw_log2FC/final_fuzzy_values/*.tsv) \
					sample_mapping.tsv \
					$(wildcard ./template_features/*.tsv) \
					./config/EM_regulators.json
	$(PYTHON) main_EM.py --input $(DATA)/miRNA/FV_raw_log2FC/final_fuzzy_values/ \
		--metadata sample_mapping.tsv \
		--template ./template_features/ \
		--config ./config/EM_regulators.json \
		--optimize_goal marker \
		--output ./output_regulators/markers/


specific_targets:	$(wildcard $(DATA)/RNA/FV_raw_log2FC/final_fuzzy_values/*.tsv) \
					sample_mapping.tsv \
					$(wildcard ./template_features/*.tsv) \
					./config/EM_targets.json
	$(PYTHON) main_EM.py --input $(DATA)/RNA/FV_raw_log2FC/final_fuzzy_values/ \
		--metadata sample_mapping.tsv \
		--template ./template_features/ \
		--config ./config/EM_targets.json \
		--optimize_goal context-specific \
		--output ./output_targets/context-specific/


marker_targets:	$(wildcard $(DATA)/RNA/FV_raw_log2FC/final_fuzzy_values/*.tsv) \
				sample_mapping.tsv \
				$(wildcard ./template_features/*.tsv) \
				./config/EM_targets.json
	$(PYTHON) main_EM.py --input $(DATA)/RNA/FV_raw_log2FC/final_fuzzy_values/ \
		--metadata sample_mapping.tsv \
		--template ./template_features/ \
		--config ./config/EM_targets.json \
		--optimize_goal marker \
		--output ./output_targets/markers/