Bug #509

Clean up runt variants imported by PharmGKB

Added by Tom Clegg almost 9 years ago. Updated over 8 years ago.

Status:
New
Priority:
Normal
Assigned To:
Target version:
-
Start date:
Due date:
% Done:

0%

Estimated time:
Billable:
Estimatedhours:
Hours:
Totalhours:
Resolution:
Story points:
-

Description

The PharmGKB importing robot has managed to create several variants that show up in reports as "CETP 1" (gene='CETP', aa_pos=1, aa_from=!_, aa_to is null), and a couple with stuff like gene='SLC1A1', aa_pos=3780412, aa_from=!_, aa_to='Ala'.

mysql> select distinct fullname from variants v
 left join edits e on v.variant_id=e.variant_id
 left join eb_users on oid=edit_oid
 where variant_aa_from=_;
+--------------------------+
| fullname                 |
+--------------------------+
| [[PharmGKB]] Importing Robot | 
+--------------------------+
1 row in set (0.10 sec)
mysql> select * from variants where variant_aa_from=_ and variant_rsid is null;

History

#1 Updated by Ward Vandewege over 8 years ago

  • Project changed from External to GET-Evidence
  • Category deleted (GET-Evidence)

#2 Updated by Madeleine Ball over 8 years ago

  • Priority changed from High to Normal

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