[Biopython-dev] Tutorial: GenomeDiagram problem

[Peter Cock]

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).

> Regarding the other problem, I do not think it is a problem with
> sending images or ipython notebook (if you scroll the example above,
> you will see plenty of pictures). I think it might be that the tutorial
> examples are not self contained. Reading the text it seems that it is
> possible to combine several pieces of code to produce some of the
> figures. But it is not clear how (at least for me).

Evidently I got the balance of verbose repetition versus clarity wrong.

The idea would be to repeat the setup steps, use the alternative
feature definition, and then repeat the output step.

Peter