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

[Jason Stajich]

It really only makes sense in the context of remoteblast - you can in fact
retrieve the report more than once and/or can put the hooks there.  In
fact with LWP the data is either memory resident with a string or saved in
a temp file - Make the user provide a filename to save the report too -
strip out so that it is only the <pre></pre> block and that should be good
enough in my opinion.

-j

On Wed, 11 Sep 2002, Wiepert, Mathieu wrote:

> 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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> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu