[EMBOSS] Plasmid drawing

[Peter Cock]

On Mon, Dec 5, 2011 at 9:26 AM, Peter Rice <pmr at ebi.ac.uk> wrote:
> On 12/05/2011 09:16 AM, Hans-Rudolf Hotz wrote:
>>
>> Thanks to the Galaxy framework, our lab scientist are using more and
>> more EMBOSS tools. Now, it would be very handy if there was an EMBOSS
>> drawing tool (even a very simple one) which takes an embl or genbank
>> file as input and creates something "colorful". By default each Key or
>> Qualifier is given a specific color and shape (eg 'arrow'). And you can
>> change them as options.
>
> Interesting suggestion. Can you send an example of what you
> would like to see?
>
> You can use your favourite drawing tool if you like, but it is OK if
> you draw it in crayon, scan it and send the image :-)
>

I use Biopython's GenomeDiagram for this sort of thing, which
internally uses a Python library called ReportLab which can
produce PDF, SVG, PNG, etc. Sadly I doubt that would be
suitable for EMBOSS which would really want a C library.

GenomeDiagram has the notion of tracks - which can be
useful for separating different types of features which would
otherwise overlap (e.g. gene/mRNA/CDS) and other tricks.
It also has some defaults about which feature qualifiers
to use as the feature name (e.g. gene, locustag).

I have considered writing a Galaxy tool to take an EMBL or
GenBank file and produce a picture, but haven't got round
to it yet.

Anyway, there may be some useful ideas for layout here
if nothing else.

Peter