#SHELL=qrsh hostname; /bin/zsh
SHELL=bash

MISC=../../scripts

AUTOSOMES=1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
CHROMOSOMES=$(AUTOSOMES) X Y
ALIGN=/depot/data1/cache/mouse/mm7/align/17-way/maf

REF=mm7
SPECIES=mm7,hg17,panTro1,rheMac1,rn3,canFam2,bosTau2
REORDER=3,0,1,2,4,5,6

REGIONS=$(CHROMOSOMES)

MODEL=test_1.063
MODSPEC=tree_pruned:N=10,D=0.01
MODORDER=2

chromlen.txt : /depot/data1/cache/chrominfo.txt 
	grep mm7 $< | tr " " "," | prefix_lines "mouse," | ./nib_location.py /depot/data1/cache/mouse/mm7/seq/%s.nib > $@

preCRM_regions.bed :
	( for f in ~/work/ross_mm7_predictions/sequences/*_mm7.txt; do head -1 $$f | egrep "chr[0-9XY]+\:[0-9]+\-[0-9]+" -o | tr ":-" "\t\t" | paste - <( basename $${f%%locus_hg17.txt} ); done ) > $@

%.scores.bz2 : %.bed
	prefix_lines "mm7." < $< \
	| ~/projects/bx-python-trunk/scripts/maf_tile_2.py $(SPECIES) chromlen.txt $(ALIGN)/chr*.maf \
	| $(MISC)/maf_translate_chars.py \
	| rp_score_maf.py /dev/stdin $(MODEL).sm /dev/stdout -m $(MODEL).mapping -w 100 -s 1 -M $(MODSPEC) -r $(REORDER) \
	| bzip2 \
	> $@

include ../common.mk