[Biopython-dev] Enhancements to Bio.Graphics.BasicChromosome

Kevin Jacobs <jacobs@bioinformed.com> bioinformed at gmail.com
Wed Oct 5 13:16:56 UTC 2011

On Mon, Oct 3, 2011 at 6:24 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Notches in the chromosome which I assume are centromeres
> (I can see how that might be added to the Bio code as another
> segment type, similar to the telomeres).

Yes-- although the visual style for centromeres need not be precisely as
shown in my example.

> Coloured background regions in the chromosome (should be
> able to do this already), some of which are hatched (not possible
> right now... would have to look into ReportLab's capabilities here).
> This is what you meant by banding?

Yes-- being able to show cytobands and custom bands to designate regions
will be very useful for me.  As before, I'm not wed to the cross-hatching,
in fact the standard displays use only grayscale.

Multiple coloured dots for labels. Doable, but a nice API might
> be tricky.

I don't much care about those -- I'd be happy with text labels.

> For layout did you mean the fact this isn't just a row of
> chromosomes left to right, but here there are two rows?
> I'm inclined to say the user should just move things in
> the PDF for a final version using Adobe of Inkscape ;)

Correct.  I'd prefer to have some programmatic control of layout, since I'd
hate to have to manually edit every whole-genome plot.  Since I'm working
exclusively with human data for now, it would be possible to pre-specify a
few standard layouts and avoid the trouble of supporting dynamic features.

Just let me know when the code is stable enough to start poking around.
 I'll float a proposal for what I think could be done to obtain feedback
before I commit much time to coding.


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