[Bioperl-l] SSEARCH Module needed? no. 2:

[Shawn Hoon]

Ok I have committed the Bio::Tools::Run::Alignment::StandAloneFasta  
module in bioperl-run

Tiequan, I have made some minor changes to your code to follow some 
bioperl conventions .
THere is no longer a showoptions/changeoptions method as now all the 
parameters
have individual accessors via the AUTOLOAD mechanisms. I have tested it 
on fasta33
(there is some thing buggy with my version of fasta34 which is printing 
some extra lines)
The .t file tests only with fasta34 however.

pls try it out and see how it works.

thanks


shawn

On Thursday, February 20, 2003, at 05:31 PM, Jason Stajich wrote:

> See the bioperl-run CVS module for all the modules which run 
> applications.
> from the FAQ
>    Q6.2: Hey, I want to run clustalw within Bioperl, I used
> 	 Bio::Tools::Run::Alignment::Clustalw before - where did it go?
>
>       A: The Bio::Tools::Run directory was moved to a new package to 
> help
> 	 make the size of the core code smaller and separate out the more
> 	 specialized nature of application running from the rest of
> 	 Bioperl.  You can get these modules by installing the bioperl-run
> 	 package.  This is either available from CVS under the same name or
> 	 available in the http://bioperl.org/DIST directory and on CPAN.
> 	 This changeover began in the bioperl 1.1 developer release.
>
> We are implementing a Fasta/SSearch run wrapper based on a submission 
> by
> tiequan zhang.  Shawn Hoon is about to commit a working version - 
> probably
> today.
>
> -jason
>
>
> On Thu, 20 Feb 2003, Konrad Foerstner wrote:
>
>> Hi!
>>
>> I have got no answer on my mail "SSEARCH Module needed?", yet. The 
>> coding
>> of the interface had finished some days ago. But I noticed, that
>> "ClustalW.pm" which I used as a template is not contained in the newer
>> versions of Bioperl. Is there any interest of my module?
>>
>> Konrad
>>
>> _______________________________________________
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>> Bioperl-l at bioperl.org
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>>
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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