[Biopython-dev] [Bug 2671] Including GenomeDiagram in the main Biopython distribution

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http://bugzilla.open-bio.org/show_bug.cgi?id=2671





------- Comment #14 from lpritc at scri.sari.ac.uk  2008-12-01 10:59 EST -------
(In reply to comment #12)
> Bio.Graphics.GenomeDiagram.DrawAll
> ==================================
> According to the comments, this is a script to walk a directory structure below
> the directory passed, and draw images of each .gbk file found there.
> 
> While useful, I don't think this belongs in the core library.  Maybe rename it
> and move it into our scripts or example directory instead...

Ah.  I thought I'd left that one out.  I was picturing perhaps having a
Utilities.py module containing a function with that behaviour, and/or functions
that drew a standard representation of a GenBank file, so that those who are
not interested in the minutiae of the API/drawing their diagrams could still
get a fair amount of function for little effort.

On reflection, these functions are perhaps better suited to living in
__init__.py.  What do you think?

> Bio.Graphics.GenomeDiagram.Utilities
> ====================================
> This is a collection of utilities for getting information useful for graph
> values,

> I can see why these were useful when GenomeDiagram was a separate package, but
> I don't think we should add this file to Biopython as it is unnecessary code
> duplication.  If we do lack any of this functionality, putting it somewhere
> under Bio.SeqUtils makes more sense than under Bio.Graphics.

Where there is repetition of function here, I'm happy to go with established
Biopython code in preference.  For graph data, GenomeDiagram expects a list of
(position, value) tuples, which the functions in Utilities.py supply directly. 
There will be a level of user-processing required in moving to the Biopython
versions.  Perhaps the inclusion of similar functions in __init__ that wrap the
Biopython versions to produce the appropriate format for graphs would be useful
here?

> I have not looked at any implications this may have for the existing
> documentation or the GenomeDiagram unit test.

Removing Utilities.py outright will affect both the documentation and the unit
test.  Both require those functions (or something similar) to generate
test/example graph data.

I would be happy to replace the existing functions with wrapped Biopython
functions in __init__ - does this seem like a sensible option?


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