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

[Antony Lee]

The restriction code does *way* more magic with metaclasses than needed
(and I don't think IPython is really to blame here as the code breaks some
fairly basic assumptions about the Python object model IMHO).  I have in
fact a PR from nearly one year ago that basically reimplemented the whole
module from scratch (https://github.com/biopython/biopython/pull/148).
 Feel free to try it.

Antony


2013/12/4 Christopher J Friedline <cfriedline at vcu.edu>

> I may have spoken too soon about the notebook specificity - got the same
> error when I run .full() on the Analysis object in the ipython console.
>
> On Wed, Dec 4, 2013 at 8:53 PM, Christopher J Friedline
> <cfriedline at vcu.edu>wrote:
>
> > 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
> >> > _______________________________________________
> >> > Biopython mailing list  -  Biopython at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/biopython
> >>
> >
> >
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