Cogent.Db.Ensembl Cookbook Example Returns 'Programmingerror', New Bug?

Question

[a1ultima]

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

[Pierre Lindenbaum]

cross posted on SO: http://stackoverflow.com/questions/21142750

Answer 1

[Emily]

Your error message suggests that you're looking at Ensembl 70, whereas you state you're looking at Ensembl 74. I'm not familiar with PyCogent but I'd guess that your error is the result of a disconnect between the database you're looking for and the database you have.

[a1ultima]

unfortunately changing that did not fix the problem, i did actually experiment with many ensembl release versions and must have pasted an error message from an upstream trial'n'error - thanks for pointing that out though, very observant!