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...
Get the latest code from the public git repository if you want to test
this...
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.
-- Chris
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