[BioPython] Generating Figures in Python

[Andrew Dalke]

Brad:
>Using the really excellent
>reportlab distribution (http://www.reportlab.com),

I've also been playing around with reportlab.  I have
this idea to use it to generate automated reports from,
say, a Genbank record, with the graphics added to show
where the features are.

Problem with that was two-fold.  I haven't done 2D
graphics in a long time and never with sequence data,
and .. I started the code and ended up doing mindy
instead, which is a bit of a tangent.

BTW, Dinu Gherman is one of the reportlab developers,
worked at EMBL, AND is a biopython reader, so I think
we have inside help with this sort of thing.

>here's an example of the type of stuff:
>
>http://www.bioinformatics.org/bradstuff/lab/cotton_locations-all.pdf

Cool!  Much better than the little bit I managed to write.
(I think I'll stay out of the 2D world for a while more :)

What I was having trouble with, btw, was figuring out
what to do when the sequence became too long for the width
of a page (assuming you wanted to see letters) or when
the annotations were too many for the height of a page.
I could think of many things to do, like use the concept
of "flowables" in Platypus, but there is little documentation
on how that works (Dinu pointed out to me at the Python
conference that my ideas garnered from reading the source
wasn' correct) and little experience from real life to
know what people want as a result.

But I do urge others to give it a try.  As Brad says,
reportlab is quite powerful and easy to use.

>This got me thinking -- is there any interest in this type
>of code for biopython? 

Sure.

Speaking of CVS, I finally got the modem <-> ethernet
gateway working and my wireless ethernet connection all
talking under both MS Windows and Linux, so I will be
putting the Martel code under CVS RSN.  And this time
I mean it!

                    Andrew
                    dalke@acm.org