[Biopython] Cross-Links in circular GenomeDiagram?

[Ilya Flyamer]

Hi Leighton,

it is good news, you have already had this idea!
To be honest I would really like to contribute to this feature, but I am
afraid, that I am not qualified enough and don't have enough experience.

Best,
Ilya


2013/11/20 Leighton Pritchard <Leighton.Pritchard at hutton.ac.uk>

>  Hi Ilya
>
>  On 19 Nov 2013, at Tuesday, November 19, 22:15, Ilya Flyamer <
> flyamer at gmail.com> wrote:
>
> The documentation says, that 'Biopython 1.59 added the ability to draw
> cross links between tracks - both simple linear diagrams as we will show
> here, but also linear diagrams split into fragments and circular
> diagrams.'  I hoped that it was possible to make crosslinks between
> fragments of the same track (as Circos can draw), but, apparently, I was
> wrong: if I try to do that, I get a NotImplementedError(). The source is
> quite explicit on this matter:
>
>        if trackobjA == trackobjB:                raise
> NotImplementedError()
>
> So, it is really not implemented.
>
>
>  Yes - the docs say "cross-links *between* tracks", rather than 'between
> two points on the same track' because of that, I'm afraid.
>
> But are there any plans on implementing Circos-style crosslinks
> (intra-track in Circular Diagram)? That would be a really useful feature
> (for me), and there are not many programmes, that can do such things.
>
>
>  It's something I've had kicking around in my head as an idea for the
> next iteration of the module, but I've not made a start. So, if anyone
> wants to dive in and implement it, they should feel free. Especially if
> they want to incorporate some cool edge bundling (e.g.
> http://blog.visualmotive.com/2009/graph-visualization-edge-bundling/).
>
>  Cheers,
>
>  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
>
>
>
>
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