[pygr-notify] Issue 76 in pygr: ensembl.SeqRegion gives KeyError if missing coord system

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Updates:
	Summary: ensembl.SeqRegion gives KeyError if missing coord system
	Status: Invalid
	Cc: marecki
	Labels: -ReviewBy-cjlee112 ReviewBy-marecki

Comment #6 on issue 76 by cjlee112: ensembl.SeqRegion gives KeyError if  
missing coord system
http://code.google.com/p/pygr/issues/detail?id=76

Hi Jenny,
just because the issue76.py script doesn't crash on the 36i dataset does  
not alter
the analysis of *why* it fails on the original dataset you reported the bug  
for,
namely that the script fails to specify one of the coordinate systems (15)  
required
for using that dataset.  You should understand that the error message arose  
only by
chance; AnnotationDB.__init__ takes the very first annotation row returned  
by the
iterator and checks that it constructs successfully, so that users will get  
an error
message immediately if they have given wrong information to the  
constructor.  If this
specific exon had not by chance been the first annotation row, this crash  
would not
have occurred.  So it's not too surprising that the same script doesn't  
generate this
crash on a different dataset.

There is a simple fix for the crash that you reported: in your issue76.py  
script, add
coord system 15 to the coordSystems argument passed to your SeqRegion  
constructor.
However, there is no way I can make this fix as part of Pygr, because the  
issue76.py
script is not part of Pygr; it is not even in the pygr git repository.  In  
fact, the
class that raises the initial error (ensembl.SeqRegion) is not part of  
Pygr, either...

The error message reported by AnnotationDB in this case seems like correct  
behavior.

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