[Tutor] Re subprocess

[jarod_v6 at libero.it]

Thanks for the suggestion and corrections.
I don't put the else staement onf if log_file but now I realize my mistake
I have 3 comand to do:
step_1_out =["STAR --genomeDir /home/sbsuser/databases/Starhg19/GenomeDir/ --
runMode alignReads --readFilesIn %s   %s  --runThreadN 12  --readFilesCommand 
zcat "%(dx[i],sn[i])]
step_2_out = ["STAR --runMode genomeGenerate --genomeDir  %s  --
genomeFastaFiles ~/databases/bowtie2Database/hg19.fa --sjdbFileChrStartEnd  %
sSJ.out.tab --sjdbOverhang 49   --runThreadN 12" %(tx[i],tx[i])]
step_3_out =["STAR --genomeDir %s --runMode alignReads --readFilesIn %s   %s  
--runThreadN 12  --readFilesCommand zcat "%(Pos2,dx,sn)]

So I need to run one step a time. cmd is the comand (step_1_out) e pi is the  
directory of the files.


def run(cmd,pi):
	import subprocess
	import time
	import logging

	logging.basicConfig(level=logging.DEBUG,format="%(asctime)s - %(name)s - %
(levelname)s - %(message)s")

	#logging.debug(" Running pipelines: %s" % (cmd))
	# setup logging
	
	tou = "log.txt"
	logfh = open(tou, "r+")
	

	p1 = subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE,stderr=logfh,
cwd=pi)

	#logging.info(" Running pipelines: %s" % (cmd))
	while True:
		if p1.poll() is None:
			time.sleep(120)
			pass
		if p1.poll()==0:
			print 'Finish this step.'
			logging.info("###################: %s %s" % (cmd,time.ctime()))
			break
		if p1.poll() is not None and p1.poll() != 0:
			raise Exception('Not working please check the error')
	# end logging
	
	logfh.close()

	return  0

I don't understand where is the  error in the code above. 

If I change the code in this way seems work
def run(cmd,pi):
		import subprocess
		import time
		import logging

		logging.basicConfig(level=logging.DEBUG,format="%(asctime)s - %(name)s - %
(levelname)s - %(messag
e)s")

		#logging.debug(" Running pipelines: %s" % (cmd))
		# setup logging
		log_file = "None"
		tou = "og.txt"
		logfh = open(tou, "r+")

		

		p1 = subprocess.Popen(cmd,shell=True,stdout=logfh,stderr=logfh,cwd=pi)
		p1.wait()
		

		#logging.info(" Running pipelines: %s" % (cmd))
		

		return  0

Someone can explain to me when we neet to choose wait or pool?
Thanks for the help