[pygr-notify] Issue 76 in pygr: cannot create an annotation object of a current ensembl feature table

[codesite-noreply at google.com]

Updates:
	Status: Invalid
	Labels: Milestone-Release0.8

Comment #4 on issue 76 by cjlee112: cannot create an annotation object of a  
current ensembl feature table
http://code.google.com/p/pygr/issues/detail?id=76

This does not appear to be a Pygr bug -- the error message appears to be  
correct.  I
used the python debugger to inspect the cause of the error more closely  
(which was
partly obscured by our error trapping):

>>> pdb.pm()
> /Users/leec/projects/pygr/pygr/annotation.py(137)__init__()
-> (repr(seqDB),))
(Pdb) self.get_annot_obj(k, self.sliceDB[k])
*** KeyError: 'unknown coordinate system 15'

The implication is that when you created the SeqRegion, you needed to  
include coord
system 15 in the coordSystems dictionary argument.

I used the mysql client to verify this:

mysql> select * from seq_region where seq_region_id=225896;
+---------------+-----------+-----------------+--------+
| seq_region_id | name      | coord_system_id | length |
+---------------+-----------+-----------------+--------+
|        225896 | NT_113964 |              15 | 204131 |
+---------------+-----------+-----------------+--------+


--
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