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Peter Cock | 14 Aug 2012 13:06
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Re: Genome Diagram Sigils, was: Default Behavior

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
(Continue reading)

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Peter Cock | 30 Aug 2012 10:16
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Re: Genome Diagram Sigils, was: Default Behavior

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
(Continue reading)

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Leighton Pritchard | 30 Aug 2012 10:51
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Re: Genome Diagram Sigils, was: Default Behavior


On 30 Aug 2012, at Thursday, August 30, 09:16, Peter Cock wrote:

On Tue, Aug 14, 2012 at 12:06 PM, Peter Cock
<p.j.a.cock <at> googlemail.com<mailto: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<mailto: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

[…]

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

Yes - I do.

L.

--
Dr Leighton Pritchard
Information and Computing Sciences Group; Weeds, Pests and Diseases Theme
DG31, James Hutton Institute (Dundee)
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:leighton.pritchard <at> hutton.ac.uk       w:http://www.hutton.ac.uk/staff/leighton-pritchard
gpg/pgp: 0xFEFC205C tel: +44(0)844 928 5428 x8827 or +44(0)1382 568827
(Continue reading)

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Peter Cock | 30 Aug 2012 12:18
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Re: Genome Diagram Sigils, was: Default Behavior

On Thu, Aug 30, 2012 at 9:51 AM, Leighton Pritchard
<Leighton.Pritchard <at> hutton.ac.uk> wrote:
>
> On 30 Aug 2012, at Thursday, August 30, 09:16, Peter Cock wrote:
>> Do people think (either of) these two sigils are worth adding
>> to the main branch?
>
> Yes - I do.
>
> L.

Done. Branch rebased and applied to master.

Peter
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Peter Cock | 30 Aug 2012 13:46
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Re: Genome Diagram Sigils, was: Default Behavior

On Thu, Aug 30, 2012 at 11:18 AM, Peter Cock <p.j.a.cock <at> googlemail.com> wrote:
> On Thu, Aug 30, 2012 at 9:51 AM, Leighton Pritchard
> <Leighton.Pritchard <at> hutton.ac.uk> wrote:
>>
>> On 30 Aug 2012, at Thursday, August 30, 09:16, Peter Cock wrote:
>>> Do people think (either of) these two sigils are worth adding
>>> to the main branch?
>>
>> Yes - I do.
>>
>> L.
>
> Done. Branch rebased and applied to master.
>
> Peter

And you can see the example in the Tutorial here,
http://biopython.org/DIST/docs/tutorial/Tutorial-dev.html#sec:gd_sigils

(These sigils all work on circular diagrams too, see
the examples made by test_GenomeDiagram.py)

Peter
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