HTML=/usr/local/apache/htdocs/Intronerator
BIN=${HOME}/bin/${MACHTYPE}

all::	nt4/i.nt4 features/sanger cDNA features/c2c xeno features/c2g
	features/i.coo

cDNA:	cDNA/allcdna.fa cDNA/allcdna.ix ra/good.txt cDNA/good.ali \
	cDNA/introns.txt
	@echo "cDNA complete"

features/c2g:	features/sanger/c2g ra/good.txt
	${BIN}/cluster ra/good.txt features/sanger/c2g features/c2g \
	${HTML}/nameless.raw.html > features/cluster.out 2>&1

xeno/cbriggsae/all.ix: xeno/cbriggsae/all.st
	${BIN}/ixxenost xeno/cbriggsae/all.st xeno/cbriggsae/all.ix

xeno/cbriggsae/i.xao: xeno/cbriggsae/all.st
	${BIN}/stToXao xeno/cbriggsae/all.st xeno/cbriggsae/

xeno: xeno/cbriggsae/all.ix xeno/cbriggsae/i.xao
	@echo "xeno complete"

features/orf2gene.txt:	features/gene_names.txt
	features/gene_names2orf2gene.pl features/gene_names.txt > features/orf2gene.txt

sanger/syn:	features/orf2gene.txt
	${BIN}/makeOrf2gene features/orf2gene.txt sanger/orf2gene sanger/syn > sanger/makeOrf2gene.out 2>&1
	${BIN}/moresyn sanger/syn features/syn features/orf2gene features/orfInfo > features/moresyn.out 2>&1

features/c2c:	sanger/CHROMOSOME_I.gff
	${BIN}/makec2c sanger features/c2c /dev/null > features/make.c2c.out 2>&1

features/c2c.ix:	features/c2c
	${BIN}/ixword3 features/c2c features/c2c.ix

features/i.coo: features/c2c 
	${BIN}/makepgo features/c2c features/ .coo

cDNA/introns.txt: ra/good.txt features/c2g.ix features/c2c.ix
	${BIN}/introns ra/good.txt cDNA/introns.gff cDNA/introns.txt \
	obsolete/altintron.txt ${HTML}/altsplice.raw.html \
	cDNA/introns.fa > cDNA/introns.out 2>&1

ra/good.txt:	cDNA/allcdna.ix
	${BIN}/refiAli ea/all.out cDNA/allcdna nt4 ra/good.txt \
	ra/bad.txt ra/cool.txt ra/err.txt 0 1000000 features/sanger/c2g \
	> ra/refiAli.out 2>&1

cDNA/good.ali:	ra/good.txt
	${BIN}/binGood ra/good.txt cDNA/good.ali > cDNA/binGood.out 2>&1
	${BIN}/ixali cDNA/good.ali cDNA/good.ix > cDNA/ixali.out 2>&1
	${BIN}/ali2alx cDNA/good.ali cDNA/ > cDNA/ali2alx.out 2>&1
	${BIN}/cdnaOff ra/good.txt cDNA/ > cDNA/cdnaOff.out 2>&1

features/sanger:	features/sanger/genes.gdf features/sanger/genes.ix \
	features/sanger/i.pgo
	@echo "features/sanger complete"

nt4/i.nt4:	sanger/CHROMOSOME_I.dna.gz
	cd nt4; \
	date >> dna2nt4.out; \
	./dna2nt4.sh >> dna2nt4.out 2>&1

features/sanger/i.pgo:	features/sanger/c2g
	date >> features/sanger/makepgo.out
	${BIN}/makepgo features/sanger/c2g features/sanger/ .pgo >> features/sanger/makepgo.out 2>&1

features/sanger/genes.ix:	features/sanger/genes.gdf
	cd features/sanger; \
	date >> indexgl.out; \
	${BIN}/indexgl genes.gdf genes.ix >> indexgl.out 2>&1

features/sanger/genes.gdf:	sanger/CHROMOSOME_I.gff
	cd sanger; \
	date >> ../features/sanger/gffgenes.out; \
	${BIN}/gffgenes ../features/sanger/c2g ../features/sanger/genes.gdf >> ../features/sanger/gffgenes.out 2>&1
	cp -p features/sanger/c2g features

features/c2g.ix: features/c2g
	${BIN}/ixword3 features/c2g features/c2g.ix

cDNA/allcdna.fa:	cDNA/mRNA_title.gb
	cd cDNA; \
	date >> gb2cdi.out; \
	${BIN}/gb2cdi mRNA_title.gb allcdna.fa allcdna.cdi >> gb2cdi.out 2>&1

cDNA/allcdna.ix:	cDNA/allcdna.fa
	cd cDNA; \
	date >> indexfa.out; \
	indexfa allcdna.fa allcdna.ix >> indexfa.out 2>&1