[Bioperl-l] SearchIO function to save raw blast output?

[Wiepert, Mathieu]

This makes sense for RemoteBlast, since the data is in a temporary file and never really seen.  Is it senseless otherwise?  Should this function be an option for RemoteBlast?  There is a bit more control given to the user when it is in SearchIO, in that they can control the outputfile names better.  In RemoteBLast it would be harder to do that, probably have to put all the results in one file.  If it is in SearchIO the user can only save some of the result files based on filters.  RemoteBlast would have to save them all.

-Mat

> -----Original Message-----
> From: Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu]
> Sent: Wednesday, September 11, 2002 2:59 PM
> To: 'bioperl-l@bioperl.org'
> Subject: [Bioperl-l] SearchIO function to save raw blast output?
> 
> 
> I want to have the option to save the blast output.  SaerchIO 
> seems to have a handle on the Blast Results file, or whatever 
> type of Search it is handling I presume.  is it fair to say 
> that this might be a good place to have a method like 
> 
> my $rc = $factory->retrieve_blast($rid);
> $rc->save_output("searchio.out");
> 
> Or is this way off, and SearchIO doesn't actually always have 
> a file or filehandle.
> 
> Is there a better name for a function like this?  Can I 
> always count on 
> 
> $self->file;
> 
> in SearchIO?  If so it is trivial to copy the output to a 
> different file (I assume)
> 
> I implemented something that works in the simple case, with 
> RemoteBlast output anyway.
> 
> -Mat
> 
> Mathieu Wiepert
> Medical Information Resources
> Mayo Foundation
> (507) 266-2317 Fax (507)-284-0360
> wiepert.mathieu@mayo.edu 
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