CODEWITHSUNDEEP
pythonbioinformatics
coder96
coder96

Reputation: 63

call a command line from script using python, Ubuntu OS

I am facing difficulties calling a command line from my script.I run the script but I don't get any result. Through this command line in my script I want to run a tool which produces a folder that has the output files for each line.The inputpath is already defined. Can you please help me?

for line in inputFile:
cmd = 'python3 CRISPRcasIdentifier.py -f %s/%s.fasta -o %s/%s.csv -st dna -co %s/'%(inputpath,line.strip(),outputfolder,line.strip(),outputfolder)
os.system(cmd)

Upvotes: 0

Views: 262

Answers (3)

geckos
geckos

Reputation: 6299

I usually do like this for static command

from subprocess import check_output

def sh(command):
    return check_output(command, shell=True, universal_newlines=True)

output = sh('echo hello world | sed s/h/H/')

BUT THIS IS NOT SAFE!!! It's vunerable to shell injection you should do

from subprocess import check_output
from shlex import split

def sh(command):
    return check_output(split(command), universal_newlines=True)

output = sh('echo hello world')

The difference is subtle but important. shell=True will create a new shell, so pipes, etc will work. I use this when I have a big command line with pipes and that is static, I mean, it do not depend on user input. This is because this variant is vunerable to shell injection, a user can input something; rm -rf / and it will run.

The second variant only accepts one command, it will not spawn a shell, instead it will run the command directly. So no pipes and such shell things will work, and is safer.

universal_newlines=True is for getting output as string instead of bytes. Use it for text output, if you need binary output just ommit it. The default is false.

So here is the full example

from subprocess import check_output
from shlex import split

def sh(command):
    return check_output(split(command), universal_newlines=True)

for line in inputFile:
    cmd = 'python3 CRISPRcasIdentifier.py -f %s/%s.fasta -o %s/%s.csv -st dna -co %s/'%(inputpath,line.strip(),outputfolder,line.strip(),outputfolder)
    sh(cmd)

Ps: I didn't test this

Upvotes: 0

AdamF
AdamF

Reputation: 2940

as mentioned before, executing command vias: os.system(command) is not recomended. please use subprocess (read in python docs about this modulesubprocess_module_docs). see the code here:

for command in input_file:
    p = subprocess.Popen(command, stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE)
    # use this if you want to communicate with child process
    # p = subprocess.Popen(command, stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE)
    p.communicate()
    # --- do the rest

Upvotes: 0

Amitai Irron
Amitai Irron

Reputation: 2065

You really want to use the Python standard library module subprocess. Using functions from that module, you can construct you command line as a list of strings, and each would be processed as one file name, option or value. This bypasses the shell's escaping, and eliminates the need to massage you script arguments before calling.

Besides, your code would not work, because the body block of the for statement is not indented. Python would simply not accept this code (could be you pasted into the questiong without the proper indentations).

Upvotes: 1

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