[Bioperl-l] Questions about BioPerl

[Ewan Birney]

On Wed, 29 Aug 2001, Hilmar Lapp wrote:

> Nathan Torkington wrote:
> > 
> > I suggested some simple wrappers to hide the Scary Object Stuff from
> > the minds of the weak.  The easiest part would be exported functions
> > to wrap the object constructors:
> > 
> >   use Bio::Perl;
> >   $seq = newseq( -seq              => "gattaca",
> >                  -desc             => "sample sequence",
> >                  -display_id       => "something",
> >                  -accession_number => "12",
> >                  -moltype          => "dna",
> >                 );
> > 
> >   $seq = genbank_seq( -id  => "MUSIGHBA1");
> >   $seq = genbank_seq( -acc => "AF303112");
> > 
> >   $in  = openseq(Fasta, "< inputfilename");
> >   $out = openseq(EMBL, "> outputfilename");
> >   $in  = openalign(fasta , "< inputfilename");
> >   $out = openalign(pfam, "> outputfilename");
> > 
> 
> Sounds good. I can imagine that there are some potential users out
> there who are on a level that pure OO would scare them off for a
> while. If this lowers the barrier, sure go ahead. Maybe the only
> reason this doesn't exist yet is the fact that those who know how
> to OO are reluctant to code this and the others who don't know are
> too scared to dare.
> 
> > 
> > If nobody points out that I've obviously been hitting the crack pipe
> > and has me committed to an asylum for the mentally cuckoo, I'll start
> > coding.
> 
> Sure, you're more than welcome. I'd put this into one module so
> that you could say 'use Bio::Perl;' or 'use Bioperl;' or even 'use
> Bio;' ;)

I think use Bio::Perl; is the ideal.

Keeps it in the Bio namespace, but looks friendly to newbies.



> 
> 	-hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                              email: hilmarl@yahoo.com
> A-1120 Vienna
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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