[gt-users] [Python]Proteic plot

[Sascha Steinbiss]

On 11/27/2009 10:08 AM, Nicolas Allias wrote:
> Hi all,

Hey Nicolas,

> I would first thanks everybody for this wonderful tool :-)

Thanks, always nice to hear that :)

> I have a question about the annotation sketch: How do you proceed for a 
> proteic alignment ? As far as I explored the code, I didn't found any 
> parameter allowing to change the axis information 3'-5'

Yes, this is still hard-coded due to the fact that the intention of
AnnotationSketch was to visualise features with respect to their
position in a genome. However, making the descriptions on the ruler axis
configurable should be very easy. I will implement this when I find the
time, making the descriptions on both ends configurable via style file
parameters. What do you think?

> Oh, another question: does anyone has the code of this wonderful picture 
> http://genometools.org/images/example_ct.png ?
> I'm more interested by the use of CustomTrack.

I assume that you have already downloaded the GenomeTools source code.
The source code for the GC content custom track can be found in the
src/annotationsketch/custom_track_gc_content* files.
Additionally, an example C program using this code and showing how to
use the custom track can be found in:
src/examples/sketch_parsed_with_ctrack.c.
This program has also been used to create the example picture you
mentioned, given example annotations and sequence from chromosome 4 of
Drosophila melanogaster.

If you prefer Ruby or Python over C, there are also custom track
examples in the gtruby/annotationsketch and gtpython/gt/annotationsketch
directories.

I am sure you will figure out how to use the custom track functionality.
Feel free to contact me again if you have any more questions.

> Thanks
> Nicolas

You're welcome!
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