Extract cool2newcool

#regions := chr8:127000000-129200000 chr14:96500000-99300000
r1=chr8:127000000-129200000
r2=chr14:96500000-99300000
#regions := chr14:96500000-99300000
binsize=10000
chrom_sizes=~/Documents/ref/chrom_GRCh38.105.sizes
in_cool=GSM4604287_1360.iced.mcool::/resolutions/10000
out_cool=~/Documents/github/seqyuan/trackc_data/tutorials/4C/GSM4604287_1360.sub.cool

subset:
    @if [ -e cool.tmp.txt ]; then \
        rm cool.tmp.txt;\
    fi
    @$(foreach regin, $(regions), cooler dump --join -r $(regin) $(in_cool) >>cool.tmp.txt;)
    cat cool.tmp.txt |cooler load --format bg2 $(chrom_sizes):$(binsize) - $(out_cool)
    #rm cool.tmp.txt

extract:
    @if [ -e cool.tmp.txt ]; then \
        rm cool.tmp.txt;\
    fi
    cooler dump --join -r $(r1) $(in_cool) >cool.tmp.txt
    cooler dump --join -r $(r2) $(in_cool) >>cool.tmp.txt
    cooler dump --join -r $(r1) -r2 $(r2) $(in_cool) >>cool.tmp.txt
    cat cool.tmp.txt |cooler load --format bg2 $(chrom_sizes):$(binsize) - $(out_cool)
    rm cool.tmp.txt

import sys,os
os.chdir('~/Documents/github/seqyuan/trackc_data/tutorials/4C')
sys.path.append('~/Documents/github/seqyuan/trackc/src')