[Biococoa-dev] Alignment & HMM Support in Biococoa

[Alexander Griekspoor]

> Incidentally, I recently wound up building OS-X versions of Muscle and
> ClustalW.  Now that our sequence object is stabilizing a bit, I was
> wondering if people thought it might be worth some effort trying to 
> write a
> generic wrapper that could feed our sequences to command line apps and 
> get a
> result back?  This would potentially help us provide a layer of 
> abstraction
> to a large number of Unix tools.
Do I understand you correctly that you want to generate a general 
NSTaskController that does the following:
BCSequence -> NSString -> Run Task with arguments -> parse output -> 
BCSequence or other objects?

> The reason this comes to mind is that I'm finding that a lot of these 
> things
> only take input in a limited number of formats, and we've already got 
> format
> conversion code in place....
The real question is how you can make the thing multipurpose instead of 
having tens of different controllers for very specific tasks... But you 
must have something in mind right?
Alex

>
> JT
>
>
>> Hi everybody,
>>
>> I'm currently working on a project focused on Hidden markov models &
>> sequence alignments.
>> I would like to contribute my work to the framework. So i'd like to 
>> add
>> aligment & HMM structures to the framework.
>>
>> What do you think about it
>>
>> Bye,
>>
>> Phil
>>
>
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                     ** Alexander Griekspoor **
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               The Netherlands Cancer Institute
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                   E-mail: a.griekspoor at nki.nl
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