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

[michael watson (IAH-C)]

OK

I have fixed my own problem (or one in Bio::DB::Query::GenBank - actually in WebQuery.pm, actually in UIR.pm!!)

IN WebQuery.pm, sub _get_request the code is:

$uri->query_form(@params)

if one does a simple "print $uri\n" we find that the url string says:

db=+nucleotide

hello?  where did that "+" come from?????  OK so if I do a $uri =~ s/\+// in my code to get rid of it, i get the correct number of results :-D

So perhaps my URI.pm is incorrect....

Mick


-----Original Message-----
From: michael watson (IAH-C) [mailto:michael.watson at bbsrc.ac.uk]
Sent: 09 September 2003 13:36
To: 'bioperl-l at bioperl.org'
Subject: [Bioperl-l] Help with Bio::DB::Query::GenBank


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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