title: Biopython blastn command not working in script, but works from command line
body: <p>So I'm writing a script to run a blast query, which I hardcoded variables for at this point (just to make sure they weren't getting messed up).  Which is:</p>
  
  <pre><code>blastCLine = NcbiblastnCommandline(query="temp.fasta", db="refseq_rna", outfmt=5, out="test.txt", evalue=0.05)
  stdt, stdr = blastCLine()
  print stdt
  print stdr
  </code></pre>
  
  <p>And I get nothing, output file is blank, and no error or anything.  If I use the blast command from blastCLine on the command line, it works.
  If i use the above code in the python environment, it works.  Just not working in my script.</p>
  
  <p>I've been googling and looking at tons of examples.  From what I can tell it should work. I've tried changing it to blastx, and using cmd="blastn" to no avail, also.
  Any suggestions?</p>