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

[Lincoln Stein]

This has been fixed in the forthcoming 1.2.3 release.  I've also corrected 
some errors in the synopsis (most importantly ids() instead of get_Ids())

Lincoln

On Tuesday 09 September 2003 08:36 am, michael watson (IAH-C) wrote:
> Hi
>
> I am having various problems with Bio::DB::Query::GenBank.
>
> I have just downloaded Bioperl 1.2.2 from the website.
>
> First of all the example gives me errors.  If i use the query string
> 'Oryza[Oragnism]', i get an error message stating that
> "<FieldNotFound>Organism</FieldNotFound>".  However, it does return a nice
> count of 5879 records.  Only if I search NCBI using the web,
> Oryza[Organism] actuallu returns 525828 records - quite significantly more
> than the 5879 that Bio::DB::Query::GenBank returns!
>
> What I am really trying to do is to get all the Gallus gallus genome
> sequences out and downloaded onto my server.  I was hoping to do this using
> Bioperl, but using "Gallus" as the query string returns 2421 using Bioperl
> and nearly 600,000 using Entrez....
>
> Can anyone please enlighten me??
>
> Thanks
>
> Mick
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-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
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Cold Spring Harbor, NY 11724
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