[Bioperl-l] Bioperl NT update

Hilmar Lapp lapp@gnf.org
Fri, 15 Dec 2000 12:41:38 -0800

Jason Stajich wrote:
> > Peter Schattner wrote:
> > > >
> > > > What is the problem with precomputed results?
> > >
> > > Perhaps I don?t understand what is meant by precomputed results.  I
> > > assumed you meant making a file with the answers that the test program
> > > expects and using those answers if the OS is non-unix.  That approach
> > > seems less maintainable than simply skipping the tests if the OS is
> > > non-unix.
> > >
> >
> > I'm not sure either what you mean. Trying to be clear, I do not mean
> > setting up a file with the output you expect from the test script. I
> > meant, instead of calling out to an executable clustalw, precompute the
> > output said executable is supposed to produce, capture it in a file and
> > feed this file into your module. This way your module can be tested on
> > any platform, and it can also be used on any platform whether or not
> > clustalw and friends are there, provided the user has means to obtain
> > the results from another machine than the one he runs bioperl on.
> >
> > This of course requires that your modules can accept either a stream
> > containing input or a pipe fed by one of the external executables.
> >
> > Am I missing something?
> The StandAloneBlast, ClustalW, and TCoffee modules are intended to be
> wrappers around actually running these programs (one of my problems with
> Bio::Tools is that we do not have a directory structure that differentiates
> processing results and running programs!) rather than processing results.
> The results processing for TCoffee and ClustalW (MSA tools) is done in
> Bio::AlignIO, while the StandAloneBlast result is sent to Bio::Tools::BPlite
> or Bio::Tools::Blast.  So there really is not way to run these on Win32 

Okay. Sorry Peter for confusing this.

What about Bio::Tools::Run as the home for modules wrapping real execution
of something?

Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757