[pygr-notify] Issue 42 in pygr: KeyError for BLAST results that return no hits

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Updates:
	Status: Fixed
	Owner: cjlee112
	Cc: ti... at idyll.org
	Labels: Milestone-Release0.8

Comment #1 on issue 42 by cjlee112: KeyError for BLAST results that return  
no hits
http://code.google.com/p/pygr/issues/detail?id=42

Hi Kenny,
thanks for reporting this.  To my mind, the problem is that the NLMSA  
interface gave
no easy way to see if the alignment was empty.  My resolution was to create  
a new
exception (EmptyAlignmentError, a subclass of ValueError), which is raised  
by NLMSA
if the user attempts to build() an alignment with no intervals.  Thus, if  
there are
no BLAST results, this exception would be raised during the blast()  
method.  If the
user wishes, he can ignore this by placing the blast() call within a  
try-except
block, like this:

from pygr.nlmsa_utils import EmptyAlignmentError
try:
     r = genome.blast(s, maxseq=1)
except EmptyAlignmentError:
     pass
else:
     # analyze the alignment results in r...

I guess we should also do something to improve the error message that you  
hit, to
explain the situation more clearly.  Presumably that error message should  
also be
changed to EmptyAlignmentError.

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