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

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Comment #3 on issue 76 by jqian.ubc: cannot create an annotation object of  
a current ensembl feature table
http://code.google.com/p/pygr/issues/detail?id=76

Hi Titus,

I cloned your seqdb_review brach:

qing at 1[seqdb_review]$ git clone git://github.com/ctb/pygr.git seqdb_review
Initialized empty Git repository in
/home/qing/workspace2009/seqdb_review/seqdb_review/.git/
remote: Counting objects: 4649, done.
remote: Compressing objects: 100% (1695/1695), done.
remote: Total 4649 (delta 3227), reused 4200 (delta 2929)
Receiving objects: 100% (4649/4649), 2.16 MiB | 319 KiB/s, done.
Resolving deltas: 100% (3227/3227), done.

Unfortunately, I still get the same error message:


qing at 1[ensembl]$ export  
PYTHONPATH='/home/qing/workspace2009/seqdb_review/seqdb_review/'

qing at 1[ensembl]$ time python issue76.py
Traceback (most recent call last):
   File "issue76.py", line 37, in <module>
     orientation='seq_region_strand'))
    
File "/home/qing/workspace2009/seqdb_review/seqdb_review/pygr/annotation.py",  
line
137, in __init__
     (repr(seqDB),))
KeyError: ' cannot create annotation object; sequence database {} may not  
be correct'


Attached is the seqregion.py.  Or, you can get it from my
git://github.com/jqian/pyensembl.git jenny_pyensembl_new branch.

Thanks,
Jenny

Attachments:
	seqregion.py  17.9 KB

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