Question

I am new to the subprocess.call function and I have tried different combinations of the same call but it is not working.

I am trying to execute the following command:

cmd = 'sort -k1,1 -k4,4n -k5,5n '+outpath+fnametempout+' > '+outpath+fnameout
print cmd

If I try the call I get an error:

cmd = cmd.split(" ")
print cmd
subprocess.call(cmd)

the error I get is:

sort: stat failed: >: No such file or directory

Answer 1

Doing it this way, you need shell=True to allow the shell redirection to work.

subprocess.call('sort -k1,1 -k4,4n -k5,5n '+outpath+fnametempout,shell=True)

A better way is:

with open(outpath+fnameout,'w') as fout: #context manager is OK since `call` blocks :)
    subprocess.call(cmd,stdout=fout)

which avoids spawning a shell all-together and is safe from shell injection type attacks. Here, cmd is a list as in your original, e.g.

cmd = 'sort -k1,1 -k4,4n -k5,5n '+outpath+fnametempout
cmd = cmd.split()

It should also be stated that python has really nice sorting facilities and so I doubt that it is actually necessary to pass the job off to sort via a subprocess.

---

Finally, rather than using str.split to split the arguments, from a string, it’s probably better to use shlex.split as that will properly handle quoted strings.

>>> import shlex
>>> cmd = "foo -b -c 'arg in quotes'"
>>> print cmd.split()
['foo', '-b', '-c', "'arg", 'in', "quotes'"]
>>> print shlex.split(cmd)
['foo', '-b', '-c', 'arg in quotes']