I too am impatient and want to monitor how my runs are going. While what people are saying above is correct that there's not a built in method, what I normally do is use watch with either grep -c or wc -l depending on your output format.

But if you want to do it in your script, either read in the file and ++ a count of "^Query=" (for standard blast format) or if you were really lazy and also didn't want to read the whole file in you could do a system call to grep the number of something like:

from subprocess import call
progressCounter = call(["grep", "-c",  "^Query=", outfile])

If you're using outfmt=8 then you could just count number of lines, or in XML there's an equivalent.

Then either output:

print "Blasting " + str(len(query)) + "sequences. Have completed " + str(progressCounter)

or do a % calc like

print "Blast is " + str((progressCounter / len(query) )*100) + "% complete"

Just some ideas.

Use Pipe Viewer

wget https://downloads.sourceforge.net/project/pipeviewer/pipeviewer/1.6.0/pv-1.6.0.tar.bz2
bzip2 pv-1.6.0.tar.bz2
tar -xvf pv-1.6.0.tar
cd pv-1.6.0
./configure
make && make install

Monitor your blast:

/path/to/pv-1.6.0/pv yourblastoutput | python yourpythonscript.py

You could add a print line before you run blast, and verify that it completed:

#!/usr/bin/env python
import os
print("Running BLAST. Please do not interrupt..")

blast = NcbipsiblastCommandline(query=sys.argv[1], db="my_db", evalue=0.0001, outfmt=5, out=name, num_alignments=100)
stdout, stderr = blastx_cline()

if os.stat('youroutputblast').st_size > 0:
         print ("BLAST complete.")
else:
         print("BLAST failed. The output is empty")

At very least, a glance at the terminal will tell one that the BLAST is still running.