[Gmod-help] insert size dependent color in gbrowse

[Scott Cain]

Hello Marvin,

I'm cc'ing this to the GBrowse mailing list, since there are lots of
Sam users on the list, and my knowledge of the internals of
Bio::DB::Sam is fairly weak.  That said, I'm going to take a crack at
this, and it may even work!

When you are executing a callback like the one you wrote below, it is
being executed on an individual feature, and it doesn't know anything
about it's mated pair.  However, it is the child of a feature that
encompasses both of the features in the pair.  In other contexts, the
parents method will return the parent object, so you can try it here
too:

fgcolor   = sub {
       my $f = shift;
       my $parent = $f->parent;
       my $insertsize = $parent->length;
...
  }

I haven't tried this, but I give it a better than 50% chance of working :-)

Scott


On Tue, Apr 27, 2010 at 2:55 AM, Mundry, Marvin <mundry at uni-muenster.de> wrote:
> hi,
> i am visualizing illumia paired end reads using Bio::DB::Sam.
> i would like to set the fgcolor of the pairs according to the insert size in order to easily identify structural variation.
>
> fgcolor       = sub {
>                       my insertsize=???
>                       if (insertsize>350) {
>                        return 'red';
>                       }else{
>                        if (insertsize<300) {
>                         return 'red';
>                        }else{
>                         return 'green';
>                        }
>                       }
>                    }
>
> how can i retrieve the insert size?
>
> regards,
>
> Marvin Mundry
> Evolutionary Bioinformatics
> Institute for Evolution and Biodiversity
> Huefferstrasse 1, D-48149 Muenster, Germany
> Phone: +49-251-83-21633
> Fax: +49-251-83-24668
> http://www.uni-muenster.de/Evolution.ebb
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research