#
#   Command file for running phylogen 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.
#
#   run_extra produces the data for the graph representation of phylogen
#   best runs (similar to Fig 3), available at the web site.
#
#   In the end, run_araCe produces the file of plain landmarks (list-formatted
#   output of phylogen for the best (a,l) values for this region, to be used in
#   displaying the alignment boxes with llat/maps (Fig. 5 of the 
#   "Comparison..." paper). Absolute paths for the files might change.
#

all:
	run_phylogen
	run_cluster
	run_expand

run_phylogen:
	ln -s /net/finch/usr/local/globin/bin/phylogen .
	phylogen alignment -I /usr/local/globin/data/align.beta  \
	-I /depot/globin/data -f tree.new -r 11240 11510 -l 9 -a 3 -o \
	-v 1.3 > phylogen.hs2.N.l9.a1.300.list
	phylogen alignment -I /usr/local/globin/data/align.beta  \
	-I /depot/globin/data -f tree.new -r 11240 11510 -l 10 -a 3 -o \
	-v 1.3 > phylogen.hs2.N.l10.a1.300.list
	phylogen alignment -I /usr/local/globin/data/align.beta  \
	-I /depot/globin/data -f tree.new -r 11240 11510 -l 11 -a 3 -o \
	-v 1.3 > phylogen.hs2.N.l11.a1.300.list

	phylogen alignment -I /usr/local/globin/data/align.beta  \
	-I /depot/globin/data -f tree.new -r 7188 7487 -l 4 -a 3 -o \
	-v 0.210 > phylogen.hs3.N.l4.a0.210.list
	phylogen alignment -I /usr/local/globin/data/align.beta  \
	-I /depot/globin/data -f tree.new -r 7188 7487 -l 4 -a 3 -o \
	-v 0.300 > phylogen.hs3.N.l4.a0.300.list 
	phylogen alignment -I /usr/local/globin/data/align.beta  \
	-I /depot/globin/data -f tree.new -r 7188 7487 -l 5 -a 3 -o \
	-v 0.210 > phylogen.hs3.N.l5.a0.210.list 
	phylogen alignment -I /usr/local/globin/data/align.beta  \
	-I /depot/globin/data -f tree.new -r 7188 7487 -l 5 -a 3 -o \
	-v 0.300 > phylogen.hs3.N.l5.a0.300.list 

	phylogen alignment -I /usr/local/globin/data/align.beta  \
	-I /depot/globin/data -f tree.new -r 64561 64826 -l 6 -a 3 -o \
	-v 0.740 > phylogen.beta.N.l6.a0.740.list
	phylogen alignment -I /usr/local/globin/data/align.beta  \
	-I /depot/globin/data -f tree.new -r 64561 64826 -l 7 -a 3 -o \
	-v 0.740 > phylogen.beta.N.l7.a0.740.list  


run_cluster:
	ln -s ../tools/cluster .
	cluster phylogen.hs2.N.l9.a1.300.list > phylogen.hs2.N.l9.a1.300.c
	cluster phylogen.hs2.N.l10.a1.300.list > phylogen.hs2.N.l10.a1.300.c
	cluster phylogen.hs2.N.l11.a1.300.list > phylogen.hs2.N.l11.a1.300.c
	cluster phylogen.hs3.N.l4.a0.210.list > phylogen.hs3.N.l4.a0.210.c
	cluster phylogen.hs3.N.l4.a0.300.list > phylogen.hs3.N.l4.a0.300.c
	cluster phylogen.hs3.N.l5.a0.210.list > phylogen.hs3.N.l5.a0.210.c
	cluster phylogen.hs3.N.l5.a0.300.list > phylogen.hs3.N.l5.a0.300.c
	cluster phylogen.beta.N.l6.a0.740.list > phylogen.beta.N.l6.a0.740.c
	cluster phylogen.beta.N.l7.a0.740.list > phylogen.beta.N.l7.a0.740.c
	rm cluster

run_expand:
	ln -s ../tools/expand .
	expand phylogen.hs2.N.l9.a1.300.c > phylogen.hs2.N.l9.a1.300.graph
	expand phylogen.hs2.N.l10.a1.300.c > phylogen.hs2.N.l10.a1.300.graph
	expand phylogen.hs2.N.l11.a1.300.c > phylogen.hs2.N.l11.a1.300.graph
	expand phylogen.hs3.N.l4.a0.210.c > phylogen.hs3.N.l4.a0.210.graph
	expand phylogen.hs3.N.l4.a0.300.c > phylogen.hs3.N.l4.a0.300.graph
	expand phylogen.hs3.N.l5.a0.210.c > phylogen.hs3.N.l5.a0.210.graph
	expand phylogen.hs3.N.l5.a0.300.c > phylogen.hs3.N.l5.a0.300.graph
	expand phylogen.beta.N.l6.a0.740.c > phylogen.beta.N.l6.a0.740.graph
	expand phylogen.beta.N.l7.a0.740.c > phylogen.beta.N.l7.a0.740.graph
	rm expand

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

run_extra: 
	interval hs2_DEVIATION.N.l9 14 > hs2_DEVIATION.N.l9.c
	int_expand hs2_DEVIATION.N.l9.c > hs2_DEVIATION.N.l9.graph
	mv hs2_DEVIATION.N.l9.* ../../results/hs2

	interval hs3_DEVIATION.N.l5 14 > hs3_DEVIATION.N.l5.c
	int_expand hs3_DEVIATION.N.l5.c > hs3_DEVIATION.N.l5.graph
	mv hs3_DEVIATION.N.l5.* ../../results/hs3

	interval beta_DEVIATION.N.l6 15 > beta_DEVIATION.N.l6.c
	int_expand beta_DEVIATION.N.l6.c > beta_DEVIATION.N.l6.graph
	mv beta_DEVIATION.N.l6.* ../../results/beta

run_araCe:
	/net/finch/usr/local/globin/bin/phylogen araCe.a \
	-I /home/galapagos/florea/test.d -f araCe_tree.def -l 8 -a 5 \
	-o -v 0.200 > tmp
	mv tmp /home/galapagos/florea/promoter.d/align.d/araCe.phylogen.a0.200.l8.list