I get an error using PyCogent to query EnsEMBl's database - I suspect this is a new bug resulting from either a new update in EnsEMBL or PyCogent.

When trying to reproduce the code for the PyCogent Cookbook's Querying Ensembl doc page ("Selecting Gene's" section) I get "ProgrammingError".

Here's the failing cookbook code (I indicate the line where error occurs):

#!/usr/bin/python
import os

#----------------------------------------------------------
# Interrogating a Genome
#----------------------------------------------------------
from cogent.db.ensembl import HostAccount, Genome
human = Genome(Species='human', Release=Release, account=account)

#----------------------------------------------------------
# Selecting Genes
#----------------------------------------------------------
brca1 = human.getGeneByStableId(StableId='ENSG00000012048') #<--- ERRORS OUT HERE
print brca1.Description

Here's the error:

ProgrammingError: (ProgrammingError) (1146, "Table 'homo_sapiens_variation_74_37.flanking_sequence' doesn't exist") 'DESCRIBE flanking_sequence' ()

Extra info:

• Python 2.7.3
• PyCogent 1.5.1-2
• Ubuntu 12.04
• Ensmbl release 74