#
#   Command file for running infocon for the best sets of (a,l) values found 
#   by the analysis. These data are represented in the blocks in Fig 4A, B, C 
#   of the "Comparison of five methods..." (Stojanovic et al) paper. 
#
#   In the end, run_araCe produces the file of plain landmarks (list-formatted
#   output of infocon for the best (a,l) values for this region, to be used in  
#   displaying the alignment boxes with llat/maps (similar to Fig. 5 of 
#   the "Comparison..." paper). Absolute paths for the files might change.
#

all:
	run_infocon 
	run_cluster
	run_expand

run_infocon:
	ln -s /net/finch/usr/local/globin/bin/infocon .
	infocon alignment -I /usr/local/globin/data/align.beta  \
	-r 11240 11510 -l 6 -a 3 -o -d 0.9 > infocon.hs2.l6.a0.900.list
	infocon alignment -I /usr/local/globin/data/align.beta  \
	-r 11240 11510 -l 7 -a 3 -o -d 0.9 > infocon.hs2.l7.a0.900.list
	infocon alignment -I /usr/local/globin/data/align.beta  \
	-r 11240 11510 -l 8 -a 3 -o -d 0.9 > infocon.hs2.l8.a0.900.list
	infocon alignment -I /usr/local/globin/data/align.beta  \
	-r 11240 11510 -l 9 -a 3 -o -d 0.9 > infocon.hs2.l9.a0.900.list
	infocon alignment -I /usr/local/globin/data/align.beta  \
	-r 7188 7487 -l 7 -a 3 -o -d 1.191 > infocon.hs3.l7.a1.191.list
	infocon alignment -I /usr/local/globin/data/align.beta  \
	-r 64561 64826 -l 6 -a 3 -o -d 1.101 > infocon.beta.l6.a1.101.list
	

run_cluster:
	ln -s ../tools/cluster . 
	cluster infocon.hs2.l6.a0.900.list > infocon.hs2.l6.a0.900.c
	cluster infocon.hs2.l7.a0.900.list > infocon.hs2.l7.a0.900.c
	cluster infocon.hs2.l8.a0.900.list > infocon.hs2.l8.a0.900.c
	cluster infocon.hs2.l9.a0.900.list > infocon.hs2.l9.a0.900.c
	cluster infocon.hs3.l7.a1.191.list > infocon.hs3.l7.a1.191.c
	cluster infocon.beta.l6.a1.101.list > infocon.beta.l6.a1.101.c
	rm cluster

run_expand:
	ln -s ../tools/expand .
	expand infocon.hs2.l6.a0.900.c > infocon.hs2.l6.a0.900.graph
	expand infocon.hs2.l7.a0.900.c > infocon.hs2.l7.a0.900.graph
	expand infocon.hs2.l8.a0.900.c > infocon.hs2.l8.a0.900.graph 
	expand infocon.hs2.l9.a0.900.c > infocon.hs2.l9.a0.900.graph
	expand infocon.hs3.l7.a1.191.c > infocon.hs3.l7.a1.191.graph
	expand infocon.beta.l6.a1.101.c > infocon.beta.l6.a1.101.graph
	rm expand

run_mv:
	mv infocon.hs2.*.c ../results/hs2
	mv infocon.hs2.*.graph ../results/hs2
	mv infocon.hs3.*.c ../results/hs3
	mv infocon.hs3.*.graph ../results/hs3
	mv infocon.beta.*.c ../results/beta
	mv infocon.beta.*.graph ../results/beta


run_araCe:
	/net/finch/usr/local/globin/bin/infocon araCe.a \
	-I /home/galapagos/florea/test.d -l 11 -a 5 -o -d 1.230 > tmp
	mv tmp /home/galapagos/florea/promoter.d/align.d/araCe.infocon.a1.230.l11.list