[Bioperl-l] problem with Bio::DB::Query::GenBank

[Hilmar Lapp]

Aaron I like this. Sounds sane, and would make things very simple for 
the user.

	-hilmar

On Friday, January 31, 2003, at 05:39  AM, Aaron J Mackey wrote:

>
> On Fri, 31 Jan 2003, Ewan Birney wrote:
>
>> I don't think this is helpful. use Bio::Perl I think should bring in 
>> all
>> necessary modules for the Bio::Perl functions to use (if not, this is 
>> a
>> bug) but ... I don't think we should import everything with a use
>> Bio::Perl.
>
> This is akin to some other packages allowing you to import the bulk of 
> its
> usability through a top-level package which simply uses the sub parts
> (e.g. Tangram, XML::Machines, etc)
>
> I think BioPerl is a bit of a beast to go "all the way" with that
> philosophy, although I could imagine that a few of the elemental *IO
> drivers could be loaded in since they themselves can perform dynamic
> loading.  Alternatively (or maybe additionally), we could make special
> EXPORT tags like:
>
> use Bio::Perl qw( :all ) # !Yikes!
> use Bio::Perl qw( :genbank ) # Bio::DB::Gen*, Bio::SeqIO, Bio::Seq, 
> etc.
> use Bio::Perl qw( :blast ) # Bio::Tools::StandAloneBlast, 
> Bio::SearchIO, Bio::Seq, etc
>
> These export tags may also qualify the methods you get (so there might 
> be
> a "bl2seq()" method you get when you import :blast):
>
>   #!/usr/bin/perl -w
>
>   # my simple BLAST aligner
>
>   use strict;
>   use Bio::Perl qw(:blast)
>   $align = bl2seq("file1.fa", "file2.fa");
>   print $align; # defaults to AlignIO::something
>   __END__
>
> -Aaron
>
> -- 
>  Aaron J Mackey
>  Pearson Laboratory
>  University of Virginia
>  (434) 924-2821
>  amackey at virginia.edu
>
>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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