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

Emmanuel Quevillon emmanuel.quevillon at versailles.inra.fr
Wed Mar 14 09:36:55 EDT 2007


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Chris Fields wrote:
> 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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> --
>> Jason Stajich
>> Miller Research Fellow
>> University of California, Berkeley
>> lab: 510.642.8441
>> http://pmb.berkeley.edu/~taylor/people/js.html
>> http://fungalgenomes.org/
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
Hi,

I just added the test script like the output (Signalp v3.0).
Can you test it from cvs?
Let me know how it goes.
Sorry I've not done it before.

Regards

- --
Emmanuel

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Emmanuel Quevillon      <emmanuel.quevillon _at versailles _inra _fr>

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