About insert shell commands into python

Question

I've inserted some shell commands into python script like below:

#!/usr/bin/python

import os,sys,re
import gzip
import commands

path = "/home/x/nearline"

for file in os.listdir(path):
  if re.match('.*\.recal.fastq.gz', file):
    fullpath = os.path.join(path, file)
    result = commands.getoutput('zcat fullpath |wc -l')
    numseqs = int(result)/4.0
  print numseqs

zcat fullpath |wc -l is the shell command inserted.

Problem is, I define fullpath here for all fastq files, but after being put under ' ', seems this fullpath doesn't work. How can I solve this problem?

Diego Sevilla · Accepted Answer · 2011-06-26 21:28:05Z

5

You have to concatenate the string with the value of the variable:

result = commands.getoutput('zcat ' + fullpath + ' |wc -l')

answered Jun 26, 2011 at 21:28

Diego Sevilla

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2 Comments

Chinmay Kanchi Over a year ago

Also, you're better off using for aFile in glob.glob(path+'/*.recal.fastq.gz') rather than bothering with os.listdir() and os.path.join().

Karl Knechtel Over a year ago

Even if there weren't the option of using glob here, the normal, simple spelling of re.match('.*\.recal.fastq.gz', file) is file.endswith('.recal.fastq.gz') (assuming you meant to escape the other dots in the regex too).

pajton · Accepted Answer · 2011-06-26 21:27:57Z

3

fullpath is a variable, you need to concatenate it with the rest of command like this:

result = commands.getoutput('zcat ' + fullpath + ' |wc -l')

answered Jun 26, 2011 at 21:27

pajton

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Comments

Evpok · Accepted Answer · 2011-06-26 21:35:48Z

1

Try

commands.getoutput('zcat ' + fullpath + ' |wc -l')

since python variables aren't auto-expanded in strings.

edited Jun 26, 2011 at 21:35

answered Jun 26, 2011 at 21:27

Evpok

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2 Comments

pajton Over a year ago

This actually won't work...you omitted spaces around fullpath

Evpok Over a year ago

True. Corrected, though I'd better delete this answer when there's 3 identical ones.

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