[Biopython-dev] Genome Diagram Sigils, was: Default Behavior

Peter Cock p.j.a.cock at googlemail.com
Thu Aug 30 08:16:13 UTC 2012

On Tue, Aug 14, 2012 at 12:06 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Thu, Aug 2, 2012 at 5:12 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Further to that work, I updated some older code for a JAGGY
> sigil, and also an OCTO sigil (names open to suggestions),
> which are on my gd-sigils branch which has documentation
> in the tutorial, including this image of the expanded sigil set:
> https://github.com/peterjc/biopython/blob/e09e264dd73953554609498c15b67d86686592fb/Doc/images/GD_sigils.png
> This is a slight simplification of the old JAGGY code in that it
> does (yet) allow control of the teeth length (e.g. to have just
> teeth on one end). I am thinking this could be exposed like
> the existing arrow specific options.
> I originally created the JAGGY sigil for marking a break point
> in a contig/scaffold. For instance, you might want to mark a
> run of NNNNN bases in a scaffold with a jaggy sigil (straddling
> both strands) as a clear visual marker to explain why there
> were no genes.
> Other sigil ideas I pondered include an OVAL, which should
> be quite easy for the linear diagrams, but rather more work to
> implement for circular diagrams due to the distorted curves.
> Peter

Do people think (either of) these two sigils are worth adding
to the main branch?

Potentially they can be generalised - the JAGGY sigil in
particular would be much more flexible if the head & tail
teeth presence (or tooth length?) could be controlled. e.g.
to draw a sigil with a flat edge on the left, and a jagged
edge on the right.


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