[Bioperl-l] Bio::Graphics - I am having trouble drawing protein domain topology

Remo Sanges sanges at biogem.it
Fri Jun 18 09:59:49 EDT 2004

On Jun 18, 2004, at 2:15 PM, Allen Liu wrote:

> Hi Bioperl-users,
> I am a bioperl newbie and I am having a hard time
> trying to get Bio::Graphics to do what I need it to.
> I have been attempting to write a script that would
> read a file like the following:
>> AAM43765	456	Bombesin	4.47E-03	307	316
>> AAM43765	456	PROTEIN_KINASE_ATP	8.00E-05	134	167
>> AAM43765	456	PROTEIN_KINASE_ST	8.00E-05	247	259
> The first column is the name of my protein.  The
> second column is the length of the protein.  The third
> column is the name of the domain.  The fourth column
> is the e-value.  The fifth and sixth columns are the
> start and ends of the domain.
> I have based my initial efforts on Lincoln Stein's
> examples which works fine and I was able to get all my
> domains on one track, but I could not get it to label
> any other domains other than the first domain.  Also,
> I could not get the solid line that links the domains
> to start from the beginning and go all the way to the
> end of the protein.

Hi Allen,

gave a quick look at your code, please consider this:

- you should open the 'panel' only once and then add all the features
   to it.

- I think that even If you EXPAND one feature, you can use only one
   description and/or score, so if you want all the domain in 
description you should
   append every time the new to the old one. In other way you can use
   different feature in order to give a description to each one.



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