[Biopython-dev] Tutorial: GenomeDiagram problem

[Peter Cock]

On Mon, May 19, 2014 at 3:52 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Mon, May 19, 2014 at 3:26 PM, Tiago Antao <tra at popgen.net> wrote:
>> Hi,
>>
>> Before I go to that problem, a somewhat more important one has
>> surfaced: The last example of the GenomeDiagram tutorial seems to have
>> a bug (either on the example code or on the module). If you scroll to
>> the end of the notebook you will see the error and will be clear.
>>
>> http://nbviewer.ipython.org/github/tiagoantao/biopython-notebook/blob/master/notebooks/17%20-%20Graphics%20including%20GenomeDiagram.ipynb
>
> Do you mean the Chromosome Diagram problem (nothing to do
> with GenomeDiagram), which you see failing with:
>
> UnboundLocalError: local variable 'fill_color' referenced before assignment
>
> Scanning the code, yes, if providing SeqFeature objects this does not
> seem to define the fill_color - which would be my fault:
> https://github.com/biopython/biopython/blob/master/Bio/Graphics/BasicChromosome.py
>
> Time to extend test_GraphicsChromosome.py to cover this...
>
> The reason we don't test this via test_Tutorial.py is the large
> data dependency (i.e. the full Arabidopsis thaliana genome).

Does this work for you now?
https://github.com/biopython/biopython/commit/8531e1c88d9e953b466a7c89009b58f77735b5d1

Thanks,

Peter