[Biodevelopers] Help finding perl scripts

[Wiepert, Mathieu]

I thought some more info from bioperl might be relevant.  Here is some text from a recent post to bioperl-l at bioperl.org

"I've checked in the first part of the Graphics HOWTO.  Where do I place 
supplementary info like figures, test data and example scripts?  Currently 
I've got all the supplementary info in docs/howto/sgml/graphics, but I'm not 
sure how this is going to work when the docbook is turned into HTML and the 
inline images go dangling."

Looks like there is some more help there maybe?

-Mat

> 
> > Dear all,
> > 
> > Where can I find some Perl scripts(or anything else)
> > that I can use to generate graphics of genetic
> > maps-bars representing linkage groups, and genetic
> > marker names at proper positions that can have hyper
> > links to other web pages? The information I have is
> > the linkage groups, distance from one end, and marker
> 
> I wish I knew more, but have you looked at GMOD, or any part 
> of it, and the Genereic Genome Browser?  Also, (I have not 
> looked), but Ensembl has pretty good graphics, and that is 
> open sourced.  I believe you can set up your own Ensembl 
> website if you wanted.  And bioperl has some graphics in it, 
> (Bio::Graphics).  Not sure how complicated you are trying to 
> be, so sorry if some of that is either overkill, or not 
> sophisticated enough
> 
> http://www.gmod.org/ggb/index.shtml
> http://www.gmod.org
> http://www.wormbase.org/db/seq/frend
> http://bio.perl.org/Core/bptutorial.html#III_8_4_Bibliographic
_objects_fo (for some reason the html is broken, actually want section III 8.5, but it is just under this).

>From the bioperl tutorial

"The Bio::Graphics::* modules use Perl's GD.pm module to create a PNG or GIF image given the SeqFeatures (Section III.7.1) contained within a Seq object.

These modules contain numerous methods to dictate the sizes, colors, labels, and line formats within the image. See Bio::Graphics, Bio::Graphics::Panel, or the scripts/render_sequence.pl script for more information.

The Genquire application also provides ways to graphically represent Seq objects (see Section IV.6). "

-mat
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