.PHONY : clean clean-db list all

REVISION = hg17 hg18 mm9 rn4 sacCer1
DBLIST = $(patsubst %,target/refseq-%.db,$(REVISION))

OUTDIR=target


all: $(DBLIST)



$(OUTDIR)/%.db: $(OUTDIR)/%.txt $(OUTDIR)/%.sql
	sqlite3 $@ < $(subst .db,.sql,$@)
	sqlite3 -separator "	" $@ ".import $< refGene"


.SECONDARY : $(OUTDIR)/refseq-sacCer1.txt.gz
$(OUTDIR)/refseq-%.txt: $(OUTDIR)/refseq-%.txt.gz
	mkdir -p $(OUTDIR)
	gunzip -c $< > $@


$(OUTDIR)/refseq-%.txt.gz: 
	mkdir -p $(OUTDIR)
	curl -o$@ http://hgdownload.cse.ucsc.edu/goldenPath/$(basename $(subst refseq-,,$(basename $(@F))))/database/refGene.txt.gz

$(OUTDIR)/refseq-%.sql: 
	mkdir -p $(OUTDIR)
	curl -o$@.orig http://hgdownload.cse.ucsc.edu/goldenPath/$(basename $(subst refseq-,,$(basename $(@F))))/database/refGene.sql
	perl mysql2sqlite.pl $@.orig > $@

clean-db:
	rm -f $(DBLIST)


clean:
	rm -rf $(OUTDIR)