[gt-users] gt-users Digest, Vol 13, Issue 7

[Sascha Steinbiss]

On 12/01/2009 09:47 AM, Nicolas Allias wrote:
> Hi all,

Hi Nicolas,

> First, thanks Sascha for your answers :-)
>>> 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.
>>>     
>> If you prefer Ruby or Python over C, there are also custom track
>> examples in the gtruby/annotationsketch and gtpython/gt/annotationsketch
>> directories.
>>   
> I'd like to test the new version, so I took the genometools-unstable 
> last modified the
> 	2009-Nov-27 11:41:39
> After having installed it, I run a test with a personal gff3 
> hand-writted... and have the same result, with the 5' 3' on the axis.

This tarball seems not to contain the changes I pushed earlier. I would
rather advise you to clone a copy from our git repository (you need the
git versioning system (http://git-scm.com) installed:

$ git clone git://genometools.org/genometools.git
$ cd genometools

Then, compile as usual.

As for your style file modifications, you can choose between
- directly changing the default style in gtdata/sketch/default.style
- making a copy of that file and modify it.

The -style option of the sketch tool (or the gt_style_load_file()
method) can be used to load a custom style file.

The new version (from the git repo) should honor the new definitions
("unit", "ruler_left_text" and "ruler_right_text").

> So I hoped I made a mistake in the file.style, so I wanted to test my 
> file.style with adding
>>     submarine      = {red=1.0, green=1.0, blue=0.0, alpha = 1.0},
> in the format block. This one is undefined but returned no errors on 
> execution. 

Since this is a perfectly fine data definition in Lua, and the style
files are essentially Lua scripts, this is not an error. Additional
key-value pairs which are not required or queried by AnnotationSketch
are simply ignored. Errors are reported only when Lua has a problem
parsing your script, e.g. in case of syntax errors.

> Have you a file.style validator?

Any Lua interpreter will do ;)

> Where am I wrong ? I'd like to see all that working :-)

I guess your problem will be gone as soon as you have the most current
version from the git repository.
Gordon, could you please update the unstable tarball to the current git
head? Unfortunately I do not have access...

> Best regards,
> Nicolas

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