[Biopython-dev] Tutorial: GenomeDiagram problem

[Tiago Antao]

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

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).

Tiago


On Mon, 19 May 2014 14:37:13 +0100 Peter Cock
<p.j.a.cock at googlemail.com> wrote:

> On Mon, May 19, 2014 at 2:26 PM, Tiago Antao <tra at popgen.net> wrote:
> > Hi,
> >
> > I am trying to produce documentation in ipython notebook as
> > previously discussed. I am currently trying to create a notebook
> > with GenomeDiagram (should look cool!)
> >
> > I have found a simple problem (not simple for me, though):
> >
> > http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec335
> >
> > On the feature captions example there is no code to actually
> > generate the picture that is there.
> >
> > I tried:
> > gdd.draw(format='linear', pagesize=(15*cm,4*cm), fragments=1,
> >          start=0, end=400)
> > gdd.write("GD_labels.png", "png")
> >
> > But with no success (either it just repeats the previous - only
> > green
> > - figure). Any ideas would be appreciated here...
> 
> Might this be something silly with reused filenames? How does
> ipython know to look at the PNG just generated?
> 
> Peter