Hey Rob,
Try to set your current directory as the first PYGRDATAPATH level for your
default PYGRDATAPATH setting. It might be cleaner than your home directory.
Jenny
On Tue, Sep 9, 2008 at 11:06 PM, Rob Kirkpatrick <
[EMAIL PROTECTED]> wrote:
> I reinstalled everything, reset all my paths and my weird error went away.
> Whoosh...like a ghost.
>
> The errors I get now are all related to pickling attempts so I'll look
> closer at this tomorrow. I'm getting 8 failures out of 24 tests.
>
>
> On Tue, Sep 9, 2008 at 7:37 PM, C. Titus Brown <[EMAIL PROTECTED]> wrote:
>
>>
>> On Tue, Sep 09, 2008 at 01:14:29PM -0700, Rob Kirkpatrick wrote:
>> -> AFAIK this is only on my machine. I'll do some cleanup and see if I
>> can get
>> -> things to go more smoothly. I only asked about the indentation because
>> most
>> -> of that code is pretty greek to me and I needed a starting point to
>> -> understand the error. I'll look at it again with your explanation and
>> see
>> -> if can grok it a bit more.
>>
>> Hi, Rob,
>>
>> using
>>
>> % nosetests --with-doctest
>>
>> everything works for me with the latest version of pygr.
>>
>> cheers,
>> --titus
>>
>> -> > > I've run into this error when trying to run some of Jenny's
>> -> > > doctests. When I look in the code of sqlgraph.py", line 269 seems
>> -> > > to be at the wrong indentation level. I get a new set of errors
>> -> > > when I indent that line, so I'm not sure if this is part of my
>> -> > > problem or not... Comments?
>> -> >
>> -> > Hi Rob,
>> -> > what makes you think line 269 is mis-indented? It looks right to me;
>> -> > __init__() must always bind its itemClass as a subclass, which is
>> what
>> -> > self.objclass() does... Note that if itemClass is None,
>> -> > self.objclass() just uses self.itemClass (typically provided by the
>> -> > class definition).
>> -> >
>> -> > more comments below...
>> -> >
>> -> > >
>> -> > >
>> -> > >
>> **********************************************************************
>> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/adaptor.py",
>> -> > > line 274, in ensembl.adaptor.ExonAdaptor
>> -> > > Failed example:
>> -> > > slice = coreDBAdaptor.fetch_slice_by_region('chromosome', '1',
>> -> > > end=100000, strand = -1)
>> -> > > Exception raised:
>> -> > > Traceback (most recent call last):
>> -> > > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> -> > > python2.5/doctest.py", line 1212, in __run
>> -> > > compileflags, 1) in test.globs
>> -> > > File "<doctest ensembl.adaptor.ExonAdaptor[5]>", line 1, in
>> -> > > <module>
>> -> > > slice = coreDBAdaptor.fetch_slice_by_region('chromosome',
>> -> > > '1', end=100000, strand = -1)
>> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
>> -> > > adaptor.py", line 688, in fetch_slice_by_region
>> -> > > sr = self._get_seqregion()
>> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
>> -> > > adaptor.py", line 584, in _get_seqregion
>> -> > > seqRegion = self._create_seqregion()
>> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
>> -> > > adaptor.py", line 565, in _create_seqregion
>> -> > > dnaAdaptor = self.get_adaptor('dna')
>> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
>> -> > > adaptor.py", line 460, in get_adaptor
>> -> > > tbAdaptor = adaptorClass(name, itemClass=rowClass,
>> -> > > serverInfo=self.conn)
>> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
>> -> > > adaptor.py", line 214, in __init__
>> -> > > sqlgraph.SQLTable.__init__(self, name,
>> -> > > itemSliceClass=seqdb.SeqDBSlice, attrAlias=dict(seq='sequence'),
>> -> > > **kwargs)
>> -> > > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> -> > > python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/
>> -> > > sqlgraph.py", line 269, in __init__
>> -> > > self.objclass(itemClass) # NEED TO SUBCLASS OUR ITEM CLASS
>> -> > > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> -> > > python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/
>> -> > > sqlgraph.py", line 352, in objclass
>> -> > > subclassArgs=dict(db=self)) # bind itemClass
>> -> > > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
>> -> > > python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/
>> -> > > classutil.py", line 217, in get_bound_subclass
>> -> > > subclass_init(**subclassArgs)
>> -> > > TypeError: unbound method _init_subclass() must be called with
>> -> > > shadowClass instance as first argument (got nothing instead)
>> -> >
>> -> > This error message seems to say that the itemClass has an
>> -> > _init_subclass() attribute that is callable, but which has not been
>> -> > "decorated" as a classmethod as it must be. For correct examples of
>> -> > how to do this, see seqdb.FileDBSequence or sqlgraph.TupleO. I guess
>> -> > I would need to scrutinize Jenny's rowClass code to verify if I'm
>> -> > interpreting this right.
>> -> >
>> -> > I don't see how this error could pass a test suite; it will die
>> -> > whenever it tries to construct an instance of this table class. Is
>> -> > this only happening on your computer, or does Jenny get the same
>> error?
>> -> >
>> -> > -- Chris
>> -> >
>> -> > >
>> -> >
>> ->
>> -> ->
>>
>> --
>> C. Titus Brown, [EMAIL PROTECTED]
>>
>>
>>
>
> >
>
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