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

[Peter Cock]

On Thu, Aug 2, 2012 at 5:12 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Thu, Aug 2, 2012 at 8:42 AM, Leighton Pritchard wrote:
>>Peter wrote:
>>>
>>> To match the current sigil argument names BOX and ARROW, I have
>>> provisionally called BIGARROW. Any better ideas?
>>>
>>
>> BIGARROW sounds fine to me. I like literal names.
>>
>
> Great. Checked into the master, and I updated the Tutorial and
> the Proux et al 2002 Figure 6 reproduction example to use this:
>
> Before (cross-links with strand specific ARROW sigil):
> http://biopython.org/DIST/docs/tutorial/images/three_track_cl2.png
>
> After (cross-links with strand straddling BIGARROW sigil):
> http://biopython.org/DIST/docs/tutorial/images/three_track_cl2a.png
>
> Original (I don't know what was used to draw this):
> http://dx.doi.org/10.1128/JB.184.21.6026-6036.2002
>
> Regards,
>
> Peter

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