[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 #12 from biopython-bugzilla at maubp.freeserve.co.uk  2008-12-01 10:47 EST -------
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...

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

    o apply_to_window (sequence, window_size, function, step=None)  Apply a
                        passed function to fragments of the passed sequence of
                        size window_size, with each window separated by the
                        passed step.

    o calc_gc_content (sequence)    Returns the %GC content of a passed
sequence

    o calc_at_content (sequence)    Returns the %AT content of a passed
sequence

    o calc_gc_skew (sequence)    Returns the GC skew of a passed sequence

    o calc_at_skew (sequence)    Returns the AT skew of a passed sequence

    o gc_content (sequence, window_size, step=None)    Returns the %GC content
                    of a passed sequence in windows of the passed size,
                    separated by the passed step size

    o at_content (sequence, window_size, step=None)    Returns the %AT content
                    of a passed sequence in windows of the passed size,
                    separated by the passed step size

    o gc_skew (sequence, window_size, step=None)    Returns the GC skew
                    of a passed sequence in windows of the passed size,
                    separated by the passed step size

    o at_skew (sequence, window_size, step=None)    Returns the AT skew
                    of a passed sequence in windows of the passed size,
                    separated by the passed step size

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.

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


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