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

[James Wasmuth]

Hi Luc,

you'll want to use the SearchIO module which is easier and more powerful 
than BPlite.  In the @params of the Blast search add '_READMETHOD' => 
'Blast'.  Then go to the HOWTO section and checkout the SearchIO.   
http://www.bioperl.org/HOWTOs/html/SearchIO.html

the output from the blastall will already be a SearchIO object if I 
remember right.


hth

J

Luc.Gauthier at aventis.com wrote:

>Hi everyone,
>
>I am currently trying to write a small tool to locally run NCBI Blast. I
>quickly found out about the "Bio::Tools::Run::StandAloneBlast" module and
>decided to use it. I am using Bioperl v1.0. Now what I would like to have as
>the final result is the plain raw blast result, as it is normally generated
>when running blast as a unix command-line tool.
>
>The reason why I want to do that is that I want to wrap that small tool as a
>SOAP web service that can be remotely called. One would call a simple method
>and get the plain raw blast result back.
>
>I am new to Bioperl and the answer to my problem may be quite simple ... I
>just can't find out how to get the raw blast report from the BPlite object
>reference I get back when calling the "blastall" method from a
>StandAloneBlast factory.
>
>Can someone help ???
>
>Thank you very much in advance and have a pleasant day !
>Luc Gauthier
>
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>

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