Looks like I'm getting the error specifically when I try to store the dna
table. If my code looks like:
serverRegistry = get_registry(host='ensembldb.ensembl.org',
user='anonymous')
coreDBAdaptor = serverRegistry.get_DBAdaptor('homo_sapiens', 'core',
'47_36i')
import pdb; pdb.set_trace()
aslice = coreDBAdaptor.fetch_slice_by_region('chromosome', '1', end=100000,
strand = -1)
And I set a breakpoint like this:
(Pdb) b pygr.classutil.get_bound_subclass
Breakpoint 1 at
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-i386.egg/pygr/classutil.py:189
Then during the first "iteration" to save seqregion, things go fine, it then
chokes when it tries to save the DNA table....
(Pdb) c
>
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-i386.egg/pygr/classutil.py(192)get_bound_subclass()
-> targetClass = getattr(obj,classattr)
(Pdb) l
187
188
189 B def get_bound_subclass(obj, classattr='__class__', subname=None,
factories=(),
190 attrDict=None, subclassArgs=None):
191 'create a subclass specifically for obj to bind its shadow
attributes'
192 -> targetClass = getattr(obj,classattr)
193 try:
194 if targetClass._shadowOwner is obj:
195 return targetClass # already shadowed, so nothing to do
196 except AttributeError: # not a shadow class, so just shadow it
197 pass
(Pdb) print obj
<SQL table homo_sapiens_core_47_36i.seq_region>
(Pdb) print classattr
itemClass
(Pdb) print subname
homo_sapiens_core_47_36i.seq_region
(Pdb) print factories
()
(Pdb) print attrDict
None
(Pdb) print subclassArgs
{'db': <SQL table homo_sapiens_core_47_36i.seq_region>}
(Pdb) c
>
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-i386.egg/pygr/classutil.py(192)get_bound_subclass()
-> targetClass = getattr(obj,classattr)
(Pdb) print obj
<SQL table homo_sapiens_core_47_36i.dna>
(Pdb) print classattr
itemClass
(Pdb) print subname
homo_sapiens_core_47_36i.dna
(Pdb) print factories
()
(Pdb) print attrDict
None
(Pdb) print subclassArgs
{'db': <SQL table homo_sapiens_core_47_36i.dna>}
(Pdb) c
TypeError: 'unbound method _init_subclass() must be called with shadowClass
instance as first argument (got nothing instead)'
> /Users/goober/pygr-dev/bin/python(23)<module>()
-> execfile(sys.argv[0])
(Pdb)
I'll keep looking to see if I can figure anything out...
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