[Biopython-dev] Bio.Graphics and GenomeDiagram

[Leighton Pritchard]

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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