[Bioperl-l] MEME/MAST parsers?

[Jason Stajich]

On Wed, 30 May 2001, Benjamin Berman wrote:

> 
> Hi there, I'm a new user (maybe developer) of BioPerl.   Does anyone
> know if BioPerl contains a parser for meme or mast?   I might write a
> module for AlignIO to get results out of a meme alignment.  Down the
> road I might do the same for mast.
> 
> Also, is there any standard way of printing debug comments?  I saw a
> "verbose" global variable so maybe that's it?

$self->warn($msg) will print out a message when $self->verbose >= 0
See Bio::Root::RootI for more info as it does different things depending
on what verbose is set to.

But I'd recomend only using that when you want a warning (like a non
fatal message, but not really debug stmts). For general
debug messages just put a 
if( $self->verbose > 0 ) {
	
}
around a print STDERR statement.  
At least this is my way of doing things, I think we're still looking for
the best ways to do this.

-Jason
> 
> Thanks a lot,
> ben.
> 
> -- 
> Benjamin Berman
> 
> Rubin Lab, 539 Life Sciences Addition
> 
> Department of Molecular and Cell Biology
> 
> University of California, Berkeley
> 
> benb@fruitfly.org
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/