[Bioperl-l] tempfile creation and Bio::Tools::Run

[Murad Nayal]

Jason Stajich wrote:
> 
> will do.  I am also adding tempfile and tempdir methods to RootI.  I will
> fix ClustalW and TCoffee to use tempfile properly and then move these
> modules to Bio::Tools::Run::Alignment

My feeling is that tempfile and tempdir would be better put in a
separate package. They are utilities that are only used by classes that
need temp file creation and not common behavior for all bioperl objects.
in my own perl library I have a FileTools package where I put all such
methods in (including methods to extract directory names, file
extensions and so on as well as methods to find executables etc. etc.).
encapsulating this behavior in a package allows me to do things like
clean up the temp files automatically when the program terminates. I
will be happy to contribute that to bioperl if there is interest. It is
not tested on NT/MAC though and will probably need some modification for
that. 
 


 
> Only problem is we'll lose our logs from cvs but we can always do some diffs
> when needed.
> 
> -Jason
> ----- Original Message -----
> From: "Peter Schattner" <schattner@alum.mit.edu>
> To: "Jason Stajich" <jason@chg.mc.duke.edu>
> Cc: <bioperl-l@bioperl.org>
> Sent: Sunday, December 17, 2000 2:49 PM
> Subject: Re: [Bioperl-l] tempfile creation and Bio::Tools::Run
> 
> > Jason Stajich wrote:
> > >
> > >
> > > As Hilmar has suggested, how about moving modules that run external
> > > applications to Bio::Tools::Run - while things that are typically
> parsing
> > > output from programs can stay in Bio::Tools.
> > >
> > > -Jason
> > >
> >
> > Fine with me, Jason.  Can you do the moving ...?  :-)
> >
> > Peter
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> > Bioperl-l@bioperl.org
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> >
> 
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-- 
Murad Nayal M.D. Ph.D.
Department of Biochemistry and Molecular Biophysics
College of Physicians and Surgeons of Columbia University
630 West 168th Street. New York, NY 10032
Tel: 212-305-6884	Fax: 212-305-6926