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

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Comment #7 on issue 76 by jqian.ubc: ensembl.SeqRegion gives KeyError if  
missing coord system
http://code.google.com/p/pygr/issues/detail?id=76

Hi Chris,

I took your advice and added all the coord systems listed in the ensembl  
coord_system
table to the coordSystems argument passed to my SeqRegion constructor (see  
attached
issue76.py).  I still got the same error message.  I'd highly appreciate it  
if you
could suggest possible causes of the problem.


Thanks,
Jenny

mysql> select * from coord_system;
+-----------------+------------+-------------+---------+------+--------------------------------+
| coord_system_id | species_id | name        | version | rank | attrib
           |
+-----------------+------------+-------------+---------+------+--------------------------------+
|              17 |          1 | chromosome  | NCBI36  |    1 |  
default_version
           |
|              15 |          1 | supercontig | NULL    |    2 |  
default_version
           |
|               4 |          1 | contig      | NULL    |    4 |
default_version,sequence_level |
|              11 |          1 | clone       | NULL    |    3 |  
default_version
           |
|             101 |          1 | chromosome  | NCBI35  |  101 |
           |
+-----------------+------------+-------------+---------+------+--------------------------------+
5 rows in set (0.16 sec)




Attachments:
	issue76.py  3.3 KB

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