Running a Bash Command in a loop in a Python Script

Question

I have this script of mine and it is for modifying some data I gather from GPS module. I run this code but it says there is a syntax error and I couldn't understand why there is an error, normally I use that bash command for parsing, can't it be used in a Python loop?

**

import serial
import struct
ser = serial.Serial("/dev/ttyUSB0", 4800, timeout = 1)
file = open("/home/pi/GPSWIFI.csv", "w")
file.write('\n')
for i in range(0,5):
       val = ser.readline();
       print >> file ,i,',',val
       cat /home/pi/GPSWIFI.csv | grep GPGGA | cut -c19-42 >GPSWIFIMODIFIED.csv
file.close()

**

Thanks in advance.

It says it is a syntax error ; File "GPSWIFII.py", line 10 cat /home/pi/GPSWIFI.csv | grep GPGGA | cut -c19-42 >GPSWIFIMODIFIED.csv — Tolga Varol
– Tolga Varol, Commented Aug 11, 2014 at 14:41
You can't just run bash commands directly like that. You need to import subprocess and set the parameter shell=True. You might find this tutorial helpful. — Dan
– Dan, Commented Aug 11, 2014 at 14:41
Because I will change the format from write to append and all the data will be separated by one line in the same file. — Tolga Varol
– Tolga Varol, Commented Aug 11, 2014 at 15:04
and do you know about how I can make the date which I acquire from ntp can be printed in front of "i" in by adding a word in print >> file ,i,',',val ? — Tolga Varol
– Tolga Varol, Commented Aug 11, 2014 at 15:06

Arusekk · Accepted Answer · 2014-08-11 14:48:19Z

2

running bash commands in python can be done using os.system function, or, more recommended, through subprocess.Popen. You can find more info here:

https://docs.python.org/2/library/subprocess.html#popen-constructor

It would be better if you used python-specific implementation instead, like this:

import serial
ser = serial.Serial("/dev/ttyUSB0", 4800, timeout = 1)
file = open("/home/pi/GPSWIFIMODIFIED.csv", "w")
file.write('\n')
for i in range(0,5):
       val = ser.readline();
       if val.find("GPGGA")==-1: continue
       print >> file ,i,',',val[18:42]
file.close()

note that slice in python (this val[18:42]) is indexed from 0

edited Aug 11, 2014 at 14:48

answered Aug 11, 2014 at 14:41

Arusekk

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