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

[Jason Stajich]

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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