[Biopython-dev] warning in NCBIWWW.py

[Andrew Dalke]

Using NCBIWWW.py I get

Bio/Blast/NCBIWWW.py:1070: UserWarning: qblast works only with blastn 
and blastp for now.
   warnings.warn("qblast works only with blastn and blastp for now.")

I'm using blastp.  Do I really need that warning?  Jeff commented


     # Is this warning useful?  If the program is blastn or blastp, the
     # warning is not necessary because the program is supported.  If
     # it is not, the script will raise an exception anyway.
     # - Jeff
     import warnings
     warnings.warn("qblast works only with blastn and blastp for now.")
     assert program == 'blastn' or program == 'blastp'


That should more likely be

   if program not in ("blastn", "blastp"):
       raise AssertionError("qblast only supports 'blastn' and 'blastp' "
                            "applications, not %r" % (program,))

assert errors are turned off if Python is run with -O so I only
use them to double check internal invariants, not as a way to
validate user input.

Also, like someone mentioned earlier, qblast uses the lower-level
httplib instead of urllib/urlib2 to do the HTTP connection to qblast.
That doesn't work on sites that depend on proxies to talk to
the outside world.

					Andrew
					dalke at dalkescientific.com