How to execute awk command by python code

Question

I've had a set of data which I want to deal with. I was trying to run a python code to execute "awk" command in linux. hoverver no matter how I try different arguments or functions, it all didn't work.

there are two different way in which I have tried, but they all didn't work. I don't know why

1)

#!/usr/bin/env python
import subprocess as sp
cmd = "awk, '{print $2 '\t' $4 '\t' $5 '\t' $6}', B3LYPD.txt"
args = cmd.split(',')
p = sp.Popen(args, stdin = sp.PIPE, stdout = sp.PIPE, stderr = sp.PIPE )

2)

#!/usr/bin/env python
import subprocess as sp
cmd = "awk, '{print $2 '\t' $4 '\t' $5 '\t' $6}'"
args = cmd.split(',')
p = sp.Popen(args, stdin = sp.PIPE, stdout = sp.PIPE, stderr = sp.PIPE )
c = p.communicate('B3LYPD.txt')
print c

If you are already programming in Python, are you sure you need to call awk? Python probably can do everything you need from awk just fine. — Lev Levitsky
– Lev Levitsky, Commented Sep 1, 2013 at 10:51
If you need a list of strings, rather than using c = "this, that, other" ; args = cmd.split(','), you can just use args = ["this", "that", "other"] and skip the split command. — Mark R. Wilkins
– Mark R. Wilkins, Commented Sep 1, 2013 at 13:23
Also, Lev's comment is right, you should be able to just read the text file line by line and use the split() function to pick out columns, if your code here is representative of your actual awk pattern. — Mark R. Wilkins
– Mark R. Wilkins, Commented Sep 1, 2013 at 13:25

NinjaDQ · Accepted Answer · 2016-03-14 06:46:30Z

7

While I agree that this is actually best done in Python, rather than invoking awk. If you really need to do this, then the actual error is with your awk.

#!/usr/bin/env python
import subprocess as sp
args = ["awk", r'{OFS="\t"; print $2,$4,$5,$6}', "B3LYPD.txt"]
p = sp.Popen(args, stdin = sp.PIPE, stdout = sp.PIPE, stderr = sp.PIPE )
print(p.stdout.readline()) # will give you the first line of the awk output

Edit: Fixed missing quote.

edited Mar 14, 2016 at 6:46

NinjaDQ

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answered Sep 1, 2013 at 13:06

user2736953

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CodeCode · Accepted Answer · 2020-04-02 15:26:49Z

2

You can use triple quotes to define the command and then shell=True in subprocess.

#!/usr/bin/env python
import subprocess as sp
cmd = """awk '{print $2"\t"$4"\t"$5"\t"$6}' B3LYPD.txt"""
p = sp.Popen(cmd, stdin=sp.PIPE, stdout = sp.PIPE, stderr = sp.PIPE,shell=True)
for l in p.stdout:
        print (l.decode())

answered Apr 2, 2020 at 15:26

CodeCode

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