[Biopython-dev] Tutorial: GenomeDiagram problem

[Peter Cock]

On Mon, May 19, 2014 at 4:44 PM, Tiago Antao <tra at popgen.net> wrote:
> On Mon, 19 May 2014 16:08:06 +0100
> Tiago Antao <tra at popgen.net> wrote:
>
>> I have to say that I am being a bit of a "monkey": mostly trying to
>> convert code blindly, so I am being a bit dumb with all this. That
>> being said, I spent a bit of time trying to see how to weave things
>> and it was not totally clear. While I could have done more effort, I
>> wonder if a Python beginner would not suffer a bit without at least a
>> paragraph explaining how to weave things.
>
> Further to this, converting much documentation available to notebook
> format is not a trivial exercise for a single person (there is a lot of
> content). So I picked the potentially more interesting bits and
> GenomeDiagram is one of them (simply because the charts look cool,
> hey!).
>
> I am also doing chapters 3, 4, 5 (seq), 9 (entrez) and 12 (popgen).
> These will be easier because there are no chart i/o (though I might
> add a few graphical things to spice things up).
>
> This is another way to say, if someone wants to volunteer to help ;) ...

Much (but not all) of the existing examples embedded within the
Tutorial.tex file are actually complete self contained and tested
examples (via test_Tutorial.py) and should just work.

The ones which are not tested either need complex dependencies,
or large datasets, or something like that. Perhaps something easier
to test is needed - for example including (embedding) Python
example scripts into the Tutorial.tex file, so that the Python examples
can be easily run directly?

Peter