[Bioperl-l] Swissprot query - Help!

[Brian Osborne]

SG,

Well, I think my example code got you into this, I think I should help you
out!

You can't actually query Swissprot this way, using those text values and
field names, you can only do these text queries using Genbank currently.
You'd use Bio::DB::Query::GenBank for this, not Bio::DB::GenBank. If you
want to query Swissprot you're limited to ids and accession numbers. I will
clarify the HOWTO, it's a bit unclear on this point.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of SG Edwards
Sent: Tuesday, March 15, 2005 1:38 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Swissprot query - Help!


Hi, sorry for the obvious question but I'm really new to Perl/BioPerl!!

I want to run a script that sends a query to swissprot and returns the list
of
sequences as Seq objects. I have tried the following code which throws an
exception 'MSG: Must speciy a value for uids to query'.

use Bio::DB::SwissProt;

$query = "Arabidopsis[ORGN] AND topoisomerase[TITL]";

$sp_obj = Bio::DB::SwissProt->new;

$stream_obj = $sp_obj->get_Stream_by_query($query);

while ($seq_obj = $stream_obj->next_seq) {
#print out the id
    print $seq_obj->display_id, "\n";
}

exit;


Any help is greatly appreciated!
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