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