[Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2480





------- Comment #27 from drpatnaik at yahoo.com  2008-09-30 18:19 EST -------
As I mentioned earlier, I am new to Python, and my usage of the subprocess is
indeed imperfect.

I tried the subprocess routine through a test.py file on a Mac OS X 10.5.5 with
Python 2.5.2, but w/o using Biopython. I had to use 'shell=True', otherwise
with 'shell=False',I get:

  File "/Lab/Laboratory/Libs/Python/lib/python2.5/subprocess.py", line 594, in
__init__
    errread, errwrite)
  File "/Lab/Laboratory/Libs/Python/lib/python2.5/subprocess.py", line 1091, in
_execute_child
    raise child_exception

With 'shell=True', it works even when there is a space in the file-path/names
of the BLAST executable, the database or the input sequence file (the escaping
of the spaces needs to be properly done).

--- test.py ---

  # Note escaping of the space characters vary for 
  my_blast_cmd = r'"/Lab/Laboratory/Libs/NCBI_blast/bin/Change loc/blastall" -p
blastn -d "\"/Lab/Laboratory/Libs/NCBI_blast/data/Change loc/My db\"" -i
/Lab/Laboratory/Libs/NCBI_blast/data/My\ seq.txt -m 7'

  import subprocess

  my_process = subprocess.Popen(my_blast_cmd, stdin=subprocess.PIPE,
stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
my_blast_result, my_blast_error = my_process.communicate('through stdin to
stdout')

  save_file = open('/Users/patnaik/Desktop/my_blast_error', "w")
  save_file.write(my_blast_error)
  save_file.close()
  save_file = open('/Users/patnaik/Desktop/my_blast_result', "w")
  save_file.write(my_blast_result)
  save_file.close()


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