Question

Hi I’m trying to execute bash command in python by importing commands module.I think I ask the same question here before. However this time it doesn’t work.
The script is as below:

#!/usr/bin/python

import os,sys
import commands
import glob

path= '/home/xxx/nearline/bamfiles'
bamfiles = glob.glob(path + '/*.bam')

for bamfile in bamfiles:
    fullpath = os.path.join(path,bamfile)
    txtfile = commands.getoutput('/share/bin/samtools/samtools ' + 'view '+ fullpath)
    line=txtfile.readlines()
    print line

this samtools view will produce (I think) .txt file

I got the errors:

Traceback (most recent call last):
  File "./try.py", line 12, in ?
    txtfile = commands.getoutput('/share/bin/samtools/samtools ' + 'view '+ fullpath)
  File "/usr/lib64/python2.4/commands.py", line 44, in getoutput
    return getstatusoutput(cmd)[1]
  File "/usr/lib64/python2.4/commands.py", line 54, in getstatusoutput
    text = pipe.read()
SystemError: Objects/stringobject.c:3518: bad argument to internal function

Seems it’s the problem with commands.getoutput

Thanks

Answer 1

A quick google search for “SystemError: Objects/stringobject.c:3518: bad argument to internal function” brings up several bug reports. Such as https://www.mercurial-scm.org/bts/issue1225 and http://www.modpython.org/pipermail/mod_python/2007-June/023852.html. It appears to be an issue with Fedora in combination with Python 2.4, but I am not exactly sure about that. I would suggest that you follow Michael’s advice and use os.system or os.popen to accomplish this task. To do this the changes in your code will be:

import os,sys
import glob

path= '/home/xxx/nearline/bamfiles'
bamfiles = glob.glob(path + '/*.bam')

for bamfile in bamfiles:
    fullpath = os.path.join(path,bamfile)
    txtfile = os.popen('/share/bin/samtools/samtools ' + 'view '+ fullpath)
    line=txtfile.readlines()
    print line