[personal] RE: [Bioperl-l] How do you change the default on Bio::DB::GenBank?

[Mark Wilkinson]

Hi Jas,

Thanks for responding.

Jason Stajich wrote:

>I'm pretty sure Lincoln has threatended to remove Bio::DB::GenBank from
>Bioperl if NCBI changes the interface again...
>
>I really don't see where you have the defaults for 'db'=> 'protein' in
>Bioperl 
>
[markw at blue9 bioperl-1.2.1]$ grep "protein" ./Bio/DB/GenBank.pm
                     'batch' => { 'db'     => 'protein',
                     'gi' => { 'db'     => 'protein',
                     'version' => { 'db'     => 'protein',
                     'single' => { 'db'     => 'protein',

I'm using version 1.2, and I just downloaded 1.2.1 and did a diff on the 
GenBank module and they are identical.  As you can see, in my copy they 
all default to 'protein'.

I think this problem is independent of the problem I was having 
simultaneously with Boulder::Genbank, just coincidentally I started 
using Bio::DB::GenBank as the fallback because of my problems with 
Boulder and noticed that I couldn't get genbank records with that 
library either...

M