if(os.path.exists(Output_file)):
os.remove(Output_file)
UW_chr_specific_file = log_dir+"/UW_"+chrName+".bed"
RG_chr_specific_file = log_dir+"/RG_"+chrName+".bed"
cmd1 = 'grep -e "^'+chrName+'\t" '+ RGLAB_MAPPABLE_FILE+' > '+RG_chr_specific_file
cmd2 = 'grep -e "^'+chrName+'\t" '+ WU_MAPPABLE_FILE+' > '+UW_chr_specific_file
commands.getstatusoutput(cmd1) #run first command
commands.getstatusoutput(cmd2) #run second command
op_file = log_dir+"/"+chrName+"_%J.output"
er_file = log_dir+"/"+chrName+"_%J.err"
cpp_cmd = 'bsub -o '+op_file+' -e '+ er_file+' -M'+memory+'000 -R"select[mem>'+memory+'] rusage[mem='+memory+']" '+ cpp_binary_file+" "+UW_chr_specific_file+" "+RG_chr_specific_file+" "+Output_file
commands.getstatusoutput(cpp_cmd)
while not os.path.exists(Output_file):
time.sleep(1)
#print cpp_cmd
GET_UNION_OF_FEATURES.visualize_overlaps(Output_file,chrName)
#clean up the log dir
files = os.listdir(log_dir)
for f in files:
fullpath = os.path.join(log_dir,f)
print fullpath
os.remove(fullpath)
#os.remove(Output_file)
print numpy.version.version
import GET_UNION_OF_FEATURES
arg = sys.argv
UW_mappable_file = arg[1]
RGLAB_mappable_file = arg[2]
result_file = arg[3]
res_file = open(result_file,'w')
print result_file
UW_coverage = GET_UNION_OF_FEATURES.get_coverage(UW_mappable_file)
RGLAB_coverage = GET_UNION_OF_FEATURES.get_coverage(RGLAB_mappable_file)
intersect = UW_coverage.intersection(RGLAB_coverage)
UW_not_RG = UW_coverage.difference(RGLAB_coverage)
RG_not_UW = RGLAB_coverage.difference(UW_coverage)
union = UW_coverage.union(RGLAB_coverage)
inter_len = len(intersect)
U_not_R_len = len(UW_not_RG)
R_not_U_len = len(RG_not_UW)
union_len = len(union)
del UW_coverage
del RGLAB_coverage
del intersect
del UW_not_RG
del RG_not_UW
res_file.write("intersection\t UW_but_not_RG\t RG_but_not_UW\t union\n ")
