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I get an error using PyCogent to query EnsEMBl's database - could this bug result from updates 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".

enter image description here

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
hello_there_andy
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1 Answers1

1

That error arises because Ensembl dropped the flanking_seq database from release 70 on. This issue was fixed in the PyCogent github repository.

Gavin
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