[Biopython] type object 'RestrictionType' has no attribute 'size'

Thu Dec 5 01:53:26 UTC 2013

Bow,

Thanks for your excellent reply and for taking the time to look - it never
occurred to me to use the regular (or IPython) REPL - because it's just not
my way of developing.  I think you're right about it not being a Biopython
bug, but I think the problems are related to the IPython notebook
specifically, rather than IPython, in general.  I downloaded the notebook
and ran it in the ipython console (%run magic), and it completes without
error.  Good catch - I'll touch base with the IPython folks.

Thanks,
Chris

On Wed, Dec 4, 2013 at 7:03 PM, Wibowo Arindrarto <w.arindrarto at gmail.com>wrote:

> Hi Christopher, Peter,
>
> Thank you for reporting the issue. After prodding around, I have to
> say this looks like a very interesting 'bug' :). I'm going to ramble a
> bit below, so I'll give a short TL;DR first:
>
> I don't think this is a bug from Biopython per se, since if you try
> the same code in a regular Python shell, it works (as Peter has
> shown). Don't get me wrong,
> I do appreciate the report in IPython notebook form (I'm a user myself
> and I think more people should use it, also for reporting bugs like
> this). But in the context of fixing the problem, I'd suggest that you
> use a regular Python shell instead.
>
> Now, that being said, let's delve in a bit into what's causing the bug
> (with a small disclaimer: these are my observations and I'm quite sure
> there are others who know more about this issue).
>
> If you see the stack
> trace of the error, you'd see that a huge chunk is coming from the
> IPython codebase. Initially I thought this was something of an
> artifact (I expected the entire stack to trace only Biopython code),
> but I was wrong. That stack trace really points to the cause of the
> problem: the way IPython displays cell results in the browser.
>
> More specifically, I've pinpointed this problem into the way IPython
> displays restriction enzymes. You can try it in your same Ipython
> notebook:
>
>    from Bio import Restriction as rst
>    rst.EcoRI
>
> The code above will never fail in a regular Python shell, but will
> fail in IPython.
>
> Why is this the case? I suspect it has something to do with the way
> Biopython's Restriction module is written. Turns out, there's already
> some nifty metaclass tricks being employed there that allows a given
> enzyme to have the class type of itself (e.g. instead of having a
> RestrictionType class with an instance called EcoRI, we have a
> metaclass RestrictionType with a class called EcoRI). To keep it
> short, IPython seems to do an attribute lookup on these metaclasses
> when it tries to display the object.  You'll notice that on line 333
> of
> /data7/cfriedline/anaconda/envs/conda/lib/python2.7/site-packages/IPython/lib/pretty.py,
> there is an expression that tries to get the class of the object to
> display:
>
>     obj_class = getattr(obj, '__class__', None) or type(obj)
>
> However, these metaclasses have not been instantiated into a class and
> thus do not have any 'size' attribute, IPython complains and raises an
> error.
>
> So to sum up, this behavior may be cause by IPython instead of
> Biopython. It's perhaps a good idea to mention this in the IPython
> forum / mailing list, too. They've been doing a very impressive job so
> far, so I have a hunch this may have popped up in one of their
> discussions.
>
> I have to admit that my metaclass chops are still very limited as
> these usually aren't required for most Python programming. But if
> you're interested this SO page
> (http://stackoverflow.com/questions/100003/what-is-a-metaclass-in-python)
> has a very easy to follow explanation about what they are and why they
> are useful.
>
> Anyway, that's enough for now I guess :).
>
> Cheers,
> Bow
>
> P.S. Peter, perhaps these other Restriction bugs are related with the
> metaclass? I've never delved that deep into the submodule's codebase,
> but it looks like there are some very interesting tidbits there.
>
> On Wed, Dec 4, 2013 at 5:48 PM, Christopher J Friedline
> <cfriedline at vcu.edu> wrote:
> > Hi everyone,
> >
> > I ran into this problem today, and wanted to bring it up to see if anyone
> > else has seen it.  Searching the archives didn't get me anywhere.  I'm
> > running a simple restriction analysis (on a random genome), and getting
> > this error. If I look for cut sites with the enzymes individually, it
> works
> > for each. However, when I put them into a RestrictionBatch, I get an
> error
> > on the class.
> >
> > type object 'RestrictionType' has no attribute 'size'
> >
> > I put an IPython notebook describing this here:
> >
> > http://nbviewer.ipython.org/gist/cfriedline/7790932
> >
> > Bio (1.6.2), IPython (1.1.0), Python (2.7.6/Anaconda 1.8)
> >
> > Any help is appreciated,
> >
> > Thanks,
> > Chris
> > _______________________________________________
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>