[Bioperl-l] Bio::Tools::Run::Signalp

Chris Fields cjfields at uiuc.edu
Tue Mar 13 15:19:35 EDT 2007


Not sure if the one Emmanuel Quevillon added to Bugzilla is updated  
for Signalp 3.0, but it is fairly recent.  It just hasn't been added  
in yet:

http://bugzilla.open-bio.org/show_bug.cgi?id=2203

Neil, could you try that one out, or file a bug with some example data?

chris

On Mar 13, 2007, at 1:34 PM, Jason Stajich wrote:

> On Mar 13, 2007, at 11:12 AM, Neil Saunders wrote:
>
>> dear BioPerlers,
>>
>> Re: my last post regarding Bio::Tools::Run::Signalp, my error came  
>> from an
>> incorrect $ENV{'SIGNALPDIR'}.
>>
>> My new error is:
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: parsing problem in signalp
>>
>> which stems from the Bio::Tools::Signalp parser.  So I'm (a)  
>> wondering whether
>> this module can parse SignalP 3.0 output and (b) still curious as  
>> to how to
>> specify parameters to signalp using the Run module.
>>
> For the parsing:
> Unfortunately, I doubt that it was written for SignalP 3.0 since it  
> was probably written before that came out and it hasn't been  
> updated much since then.   I think it needs a owner at this point  
> as well as the original devs on this have moved on.
> Can you perhaps provide good example files for 3.0 output?
>
> For the Running:
> It was written quite a while ago by the fugu folks and I think they  
> just hardcoded the parameters -- if you look at
> _run code you see this in the setup string:
> "-t euk -trunc 50 "
>
> So this is an example of an orphaned module that needs someone to  
> bring it up to date with the current standards of the bioperl-run  
> package.
> Sorry to not have better news than that....
>
> -j
>
>> thanks,
>> Neil
>> -- 
>>   School of Molecular and Microbial Sciences
>>   University of Queensland
>>   Brisbane 4072 Australia
>>
>> http://nsaunders.wordpress.com
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>
> --
> Jason Stajich
> Miller Research Fellow
> University of California, Berkeley
> lab: 510.642.8441
> http://pmb.berkeley.edu/~taylor/people/js.html
> http://fungalgenomes.org/
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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