[Bioperl-l] Re: bioperl pipeline picking momentum

[James Gilbert]

On Fri, 12 Apr 2002, Elia Stupka wrote:

> 1)Making the system very flexible in terms of where the input data comes
> from and where the output results should be stored. This used to be all in
> one mysql db, now it should be able to come from anywhere provided
> adaptors are in place to communicate to the resource. 
> [already underway]

One small thing I noticed yesterday when I was
coding a new Runnable was that a number of modules
are printing status / error messages to STDOUT,
not STDERR.  So when I did this:

	./test_script > results.out

results.out had the data I wanted plus reams of
rubbish.  We never see this in Ensembl becasue the
data is written to the database, and STDOUT plus
STDERR go into the same pot.

Please everyone print their status / error
messages to STDERR!

	James

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
James G.R. Gilbert            The Wellcome Trust Sanger Institute
Fax: +44 (0)1223 494919              Wellcome Trust Genome Campus
Tel: +44 (0)1223 494906              Hinxton, Cambridge, CB10 1SA