How to pass shell script`s arguments when calling BBMap from Python?
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Entering edit mode
6.4 years ago
elvissober ▴ 20

How to pass shell script`s arguments when calling BBMap from Python? Trying to call BBMap from Python 2.7. There are subprocess and os modules for that. All efforts are wrong.

Here is a code:

import os
import subprocess

os.chdir(r"/home/user/Documents/bbmap") # changing the directory to run subsequent scripts
os.system("bbmap.sh ref=fake.fa") # 1st way
process=subprocess.Popen(['bbmap.sh',str(ref=fake.fa),shell=True,stdin=PIPE,stderr=PIPE) # 2 attempt
subprocess.call('bbmap.sh, ref=fake.fa') # 3hrd way

What code can do this job?

 

sequencing python soft shell bash • 1.7k views
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0
Entering edit mode
6.4 years ago

The syntax for the 2nd and 3rd way is wrong and you'll get an error. Unless you care what it write to stdout or stderr then just use subprocess.call()

BTW, this is just a python question, you might try a python forum next time.

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Entering edit mode

what arguments to pass to subprocess.call()? thx

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