[pygr-notify] Issue 56 in pygr: unable to access the sequence object via a saved bound schema attribute :(

[codesite-noreply at google.com]

Comment #2 on issue 56 by cjlee112: unable to access the sequence object  
via a saved bound schema attribute :(
http://code.google.com/p/pygr/issues/detail?id=56

Another possible difference between Jenny's test code and my test code is  
that she
left out a required field (start) from the sliceAttrDict for both  
exonAnnoDB and
transcriptAnnoDB.  It's possible that leaving out that field caused the  
error she
reported, since that would indeed screw up its ability to access the  
sequence for the
exon annotation.

Specifically, she had:
exonAnnoDB = seqdb.AnnotationDB(exonTB, sr,
                                 sliceAttrDict=dict(id='seq_region_id',
                                                    stop='seq_region_end',
                                                     
orientation='seq_region_strand'))

whereas it should be:
exonAnnoDB = seqdb.AnnotationDB(exonTB, sr,
                                 sliceAttrDict=dict(id='seq_region_id',
                                                    start='seq_region_start',
                                                    stop='seq_region_end',
                                                     
orientation='seq_region_strand'))

This may very well be the explanation of the error message she reported.   
Jenny could
test that by seeing if removing the start entry from the sliceAttrDict in my
issue56.py code will cause the error to reproduce again...  If so, perhaps  
we should
improve the error message provided in this case; it should specifically  
tell the user
that the required start attribute was missing.

--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings