OE=$(HOME)/Eclipse/workspace/OBO-Edit2/launch_scripts
BASE=gene_ontology_xp_regulates

$(BASE)-nr.obo: ../ontology/gene_ontology_edit.obo
	$(OE)/obo2obo -allowdangling -semanticparse -o $@ $< > regulation-report.txt
.PRECIOUS: $(BASE)-nr.obo

$(BASE).obo: $(BASE)-nr.obo
	cat $< regulation_relations.obo | obol-replace-partof-with-regulates.pl > $@.tmp && mv $@.tmp $@
#	cat $< regulation_relations.obo > $@.tmp && mv $@.tmp $@
.PRECIOUS: $(BASE).obo

$(BASE)-pre_reasoned.obo: $(BASE).obo
	$(OE)/obo2obo -o -saveimpliedlinks $@ $<
.PRECIOUS: $(BASE)-pre_reasoned.obo

$(BASE)-pre_reasoned2.obo:  ../ontology/gene_ontology_edit.obo
	$(OE)/obo2obo -allowdangling -semanticparse -o -saveimpliedlinks $@ $< > regulation-report2.txt

$(BASE)-pre_reasoned-no-intersections.obo: $(BASE)-pre_reasoned.obo
	grep -v ^intersection_of $< > $@

# RUN OE TO REMOVE redundancies
regulation-nugo.obo: saved.obo
	obol-remove-regulates-relations.pl $< > $@.tmp && mv $@.tmp $@

regulation-unimplied-report.txt: $(BASE).obo
	blip -i $< -u query_go findall unimplied_reg/2 > $@.tmp && mv $@.tmp $@