[Bioperl-l] Questions about BioPerl

[Hilmar Lapp]

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;' ;)

	-hilmar
-- 
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Hilmar Lapp                              email: hilmarl@yahoo.com
A-1120 Vienna
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