I'm using python 2.6.4, ipython 0.13, and pycogent 1.5.1. When I try to get a gene by stable ID I get an error that boils down to "Table 'homo_sapiens_core_68_37.gene_stable_id' doesn't exist". This is because it doesn't. Ensembl changes the database structure going from v66 to v67 and this table was a casualty.

Unless there is a more recent version of pycogent that this is fixed in, this is a major problem. Am I missing something?

nanna.cluster.lifesci.dundee.ac.uk > /sw/bin/ipython
Python 2.6.4 (r264:75706, Sep 10 2010, 16:37:14)
Type "copyright", "credits" or "license" for more information.
IPython 0.13 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.
In [1]: import cogent.db.ensembl
In [2]: cogent.db.ensembl.__version__
Out[2]: '1.5.1'
In [3]: compara = Compara(["human","chicken"], Release=68)
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-3-eaa3c6aed488> in <module>()
----> 1 compara = Compara(["human","chicken"], Release=68)
NameError: name 'Compara' is not defined
In [4]: from cogent.db.ensembl import *
In [5]: compara = Compara(["human","chicken"], Release=68)
In [6]: egene = compara.Human.getGeneByStableId(StableId="ENSG00000111642")
---------------------------------------------------------------------------
ProgrammingError                          Traceback (most recent call last)
<ipython-input-6-0d70b62abba8> in <module>()
----> 1 egene = compara.Human.getGeneByStableId(StableId="ENSG00000111642")
/sw/opt/lib/python2.6/site-packages/cogent/db/ensembl/genome.pyc in getGeneByStableId(self, StableId)
    209     def getGeneByStableId(self, StableId):
    210         """returns the gene matching StableId, or None if no record found"""
--> 211         query = self._get_gene_query(self.CoreDb, StableId=StableId)
    212         try:
    213             record = list(query.execute())[0]
/sw/opt/lib/python2.6/site-packages/cogent/db/ensembl/genome.pyc in _get_gene_query(self, db, Symbol, Description, StableId, BioType, synonym, like)
    187         xref_table = [None, db.getTable('xref')][db.Type == 'core']
    188         gene_table = db.getTable('gene')
--> 189         gene_id_table = db.getTable('gene_stable_id')
    190
    191         assert Symbol or Description or StableId or BioType, "no valid argument provided"
/sw/opt/lib/python2.6/site-packages/cogent/db/ensembl/database.pyc in getTable(self, name)
     41         table = self._tables.get(name, None)
     42         if table is None:
---> 43             c = self._db.execute("DESCRIBE %s" % name)
     44             custom_columns = []
     45             for r in c.fetchall():
/homes/nschurch/cluster_installs/python_modules/SQLAlchemy-0.6.7/SQLAlchemy-0.6.7-py2.6.egg/sqlalchemy/engine/base.pyc in execute(self, statement, *multiparams, **params)
   1786
   1787         connection = self.contextual_connect(close_with_result=True)
-> 1788         return connection.execute(statement, *multiparams, **params)
   1789
   1790     def scalar(self, statement, *multiparams, **params):
/homes/nschurch/cluster_installs/python_modules/SQLAlchemy-0.6.7/SQLAlchemy-0.6.7-py2.6.egg/sqlalchemy/engine/base.pyc in execute(self, object, *multiparams, **params)
   1189                                                 object,
   1190                                                 multiparams,
-> 1191                                                 params)
   1192         else:
   1193             raise exc.InvalidRequestError(
/homes/nschurch/cluster_installs/python_modules/SQLAlchemy-0.6.7/SQLAlchemy-0.6.7-py2.6.egg/sqlalchemy/engine/base.pyc in _execute_text(self, statement, multiparams, params)
   1285                                 statement=statement,
   1286                                 parameters=parameters)
-> 1287         return self.__execute_context(context)
   1288
   1289     def __execute_context(self, context):
/homes/nschurch/cluster_installs/python_modules/SQLAlchemy-0.6.7/SQLAlchemy-0.6.7-py2.6.egg/sqlalchemy/engine/base.pyc in __execute_context(self, context)
   1300                             context.cursor,
   1301                             context.statement,
-> 1302                             context.parameters[0], context=context)
   1303
   1304         if context.compiled:
/homes/nschurch/cluster_installs/python_modules/SQLAlchemy-0.6.7/SQLAlchemy-0.6.7-py2.6.egg/sqlalchemy/engine/base.pyc in _cursor_execute(self, cursor, statement, parameters, context)
   1399                                 parameters,
   1400                                 cursor,
-> 1401                                 context)
   1402             raise
   1403
/homes/nschurch/cluster_installs/python_modules/SQLAlchemy-0.6.7/SQLAlchemy-0.6.7-py2.6.egg/sqlalchemy/engine/base.pyc in _cursor_execute(self, cursor, statement, parameters, context)
   1392                                 statement,
   1393                                 parameters,
-> 1394                                 context)
   1395         except Exception, e:
   1396             self._handle_dbapi_exception(
/homes/nschurch/cluster_installs/python_modules/SQLAlchemy-0.6.7/SQLAlchemy-0.6.7-py2.6.egg/sqlalchemy/engine/default.pyc in do_execute(self, cursor, statement, parameters, context)
    297
    298     def do_execute(self, cursor, statement, parameters, context=None):
--> 299         cursor.execute(statement, parameters)
    300
    301     def is_disconnect(self, e):
/sw/lib/python2.6/site-packages/MySQLdb/cursors.pyc in execute(self, query, args)
    172             del tb
    173             self.messages.append((exc, value))
--> 174             self.errorhandler(self, exc, value)
    175         self._executed = query
    176         if not self._defer_warnings: self._warning_check()
/sw/lib/python2.6/site-packages/MySQLdb/connections.pyc in defaulterrorhandler(***failed resolving arguments***)
     34     del cursor
     35     del connection
---> 36     raise errorclass, errorvalue
     37
     38 re_numeric_part = re.compile(r"^(\d+)")
ProgrammingError: (ProgrammingError) (1146, "Table 'homo_sapiens_core_68_37.gene_stable_id' doesn't exist") 'DESCRIBE gene_stable_id' ()

This is a known bug that has been fixed in the svn repository. Instructions for getting access to the repository are here.

With the latest svn revision, I get:

>>> from cogent.db.ensembl import *
>>> compara = Compara(["human","chicken"], Release=68)
>>> egene = compara.Human.getGeneByStableId(StableId="ENSG00000111642")
>>> print egene
Gene(Species='Homo sapiens'; BioType='protein_coding'; Description='chromodomain helicase DNA...'; StableId='ENSG0000011164
2'; Status='KNOWN'; Symbol='CHD4')
>>>

Cheers. I ended up rolling my own wrapper script for a straight sql query in end, but its nice to know pycogent has caught the repo version.