[Biopython-dev] Bio.Graphics and GenomeDiagram

[Robert Cadena]

I'd been working on and off on writing clones of bioperl's and
bioruby's graphics libraries:
http://www.bioperl.org/wiki/HOWTO:Graphics
http://bio-graphics.rubyforge.org/

I have very rudimentary drawing of tracks and vertically shifting
subfeatures as can be seen here:
http://machine501.com/images/bio_graphics_test_1.jpg

The prep code to draw that is very similar to the bioruby example:
--
p = Panel(100, start=10, width=480, pad_left=10, pad_right=10)

generic_track = p.add_track('generic', glyph=GenericGlyph, label="Constant")
directed_track = p.add_track('directed', glyph=DirectedBoxGlyph,
label="Variable Test")

generic_track.add_feature(SeqFeature(FeatureLocation(250, 375), 'clone1'))
generic_track.add_feature(SeqFeature(FeatureLocation(54, 124), 'clone2'))
---

I'd be happy to volunteer some time to help with GenomeDiagram and
maybe there's the possibility of incorporating the bit of code I have
to create a bioperl::graphics library clone.

thanks.

/r


On Wed, Oct 15, 2008 at 3:39 AM, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
> On 15/10/2008 11:24, "Peter" <biopython at maubp.freeserve.co.uk> wrote:
>
>> On Wed, Oct 15, 2008 at 11:00 AM, Leighton Pritchard <lpritc at scri.ac.uk>
>> wrote:
>>> Hi,
>>>
>>> A while ago I wrote the GenomeDiagram library for drawing images of genomes
>>> and other large biological sequences, and collections of sequences
>>> (http://bioinf.scri.ac.uk/lp/programs.php#genomediagram).  ...
>>> Now that I have managed to free up a little bit of time I'd like to revisit
>>> GenomeDiagram, tidy up the internals some more ..., and contribute it
>>> to Bio.Graphics ..
>>> I suggested something doing similar a while ago and got no feedback - does
>>> anyone object to this contribution, in principle or in practice?  Or are
>>> there any other comments?  I'm all (well, mostly) ears...
>
>> One small thing I would change is switching colour to color for the
>> argument/properties (the American spelling of color is the norm in all
>> programming usage).
>
> <grin> Fair point - I'll do that.  Though, like those pesky Canadians (see
> Maple), I'm inclined to permit either spelling out of sheer
> bloody-mindedness ;).  Historically (rather than etymologically), it's a
> holdover from working with interim EMBL-ish .tab files from Sanger, which
> use the British English spelling:
>
> """
> FT                   /class="3.1.03"
> FT                   /colour=7
> FT                   /gene="asnA"
> """
>
> Would people see permitting either form of colour/color as potentially
> confusing?  If so, I'm happy to go with the majority spelling.
>
>> Anyone using the existing stand alone
>> GenomeDiagram library would have to make some small changes anyway
>> (new import statements), so if there are going to be any other API
>> changes it would be best to do them at the same time.
>
> I agree.  I see this as a break from the standalone library, and would be
> branching this version of GenomeDiagram from what had gone before.  While
> I'd like to make API changes as low-impact as possible, I'm in favour of
> such changes where they support functional improvement.
>
> Cheers,
>
> L.
>
> --
> Dr Leighton Pritchard MRSC
> D131, Plant Pathology Programme, SCRI
> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
> e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
>
>
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