Python: unix system calling

Labels: Informatics
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http://docs.python.org/library/subprocess.html

[1] using subprocess

e.g. subprocess.call( ["grep", "-w", "query","file"])

import subprocess
import os

from subprocess import Popen
from subprocess import PIPE

q1 = "xxx"

q2 = "yyy"

file = "file

##

# grep -w q1 file | grep q2

#
p1 = Popen(["grep","-w",q1,file], stdout=PIPE)
p2 = Popen(["grep", q2], stdin=p1.stdout, stdout=PIPE)
p1.stdout.close()  # Allow p1 to receive a SIGPIPE if p2 exits.
output = p2.communicate()[0]
print output


[2] using os.system


import os
cmdln =  "grep -w " + q1_c + " " + db + " | grep -w " + q2_c + "|  awk -F\"\t\" '{print $1}'  "
os.system( cmdln )

---> this is not "quiet mode". quite problematic



[3] using commands

cmdln = "grep -w " + q1_c + " " + db + " | grep -w " + q2_c + "|  awk -F\"\t\" '{print $1}'  "
out = commands.getstatusoutput( cmdln )  # or simply getoutput
status = out[0]  # this is error code
bingo = out[1]   # retrieved data

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Labels: Informatics