[gt-users] [Python]Proteic plot

[Sascha Steinbiss]

On 12/02/2009 04:46 PM, Nicolas Allias wrote:
> Hi all,

Hi Nicolas,

> So I have another one : is there any parameter to force display of the 
> whole sequence ?

When creating a GtDiagram, you can specify a range which determines the
plotted region. See the interface here (from
src/annotationsketch/diagram_api.h):

GtDiagram* gt_diagram_new(GtFeatureIndex *feature_index,
                          const char *seqid,
                          const GtRange *range,
                          GtStyle *style, GtError*);

So if you want to plot the region from 100-100000 regardless of the
number and location of contained features, just pass this range explicitly:

GtRange qry_rng = {100, 100000};
...
GtDiagram *d = gt_diagram_new(feature_index, seqid, &qry_rng, style,
                              err);
...

The 'gt sketch' tool (src/annotationsketch/gt_sketch.c) also has -start
and -end options which allow to change this region. I guess you could do
it the same way in your program.

I hope this answers your question.

Best regards,
Sascha

-- 
Sascha Steinbiss
Center for Bioinformatics
University of Hamburg
Bundesstr. 43
20146 Hamburg
Germany

Email:  steinbiss at zbh.uni-hamburg.de
URL:    http://www.zbh.uni-hamburg.de/steinbiss
Phone:  +49 (40) 42838 7322
FAX:    +49 (40) 42838 7312