How to call a program installed on linux from within python?

Question

This is what I've been trying

def test():
    import sys
    import subprocess
    file1 = open(sys.argv[1],"r") #this is the input to fastacmd
    idx = file1.readlines()
    outname = idx[0].split("\r\n")[0]
    foutname = outname + "_f_output"
    astaseq = subprocess.call(["fastacmd","-i", file1, "-o",foutname])
    blastresult = subprocess.call(["blastp", "-db", "db1.faa", "-query", foutname, "-out", outname])

But I get caught with this, and I can't really make sense of it

File "test.py", line 16, in <module>
    fastacmd_blastp()
  File "test.py", line 11, in test
    fastaseq = subprocess.call(["fastacmd","-i", file1, "-o",fastaoutname])
  File "/usr/local/lib/python2.7/subprocess.py", line 486, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/local/lib/python2.7/subprocess.py", line 672, in __init__
    errread, errwrite)
  File "/usr/local/lib/python2.7/subprocess.py", line 1202, in _execute_child
    raise child_exception
TypeError: execv() arg 2 must contain only strings

Can anyone help? thanks

Change file1 to idx in that line (or perhaps sys.argv[1]?) — Koterpillar
– Koterpillar, Commented Jun 18, 2013 at 10:59

Atmaram Shetye · Accepted Answer · 2013-06-18 11:10:02Z

2

Guess the input file should be the filename sys.argv[1] and not the python handle to the file. (http://nebc.nerc.ac.uk/bioinformatics/documentation/blast/fastacmd.html)

In other words, change astaseq = subprocess.call(["fastacmd","-i", file1, "-o",foutname]) to astaseq = subprocess.call(["fastacmd","-i", sys.argv[1], "-o",foutname])

answered Jun 18, 2013 at 11:10

Atmaram Shetye

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