[Bioperl-l] Bio::Graphics - I am having trouble drawing protein
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.
gave a quick look at your code, please consider this:
- you should open the 'panel' only once and then add all the features
- 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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