[Bioperl-l] Beginners HOWTO query a range of lengths 0:3000[SLEN]

Alexander Ptok alexanderptok at web.de
Wed Jan 9 10:34:56 EST 2008


Hi,

I am a beginner to BioPerl and working through the Beginners HOWTO

Version of BioPerl is 1.4-1 running on Debian etch

In the Howto everything worked fine until the section

Retrieving multiple sequences from a database

from where i copied the following script:

use Bio::DB::GenBank;
use Bio::DB::Query::GenBank;
 
$query = "Arabidopsis[ORGN] AND topoisomerase[TITL] and 0:3000[SLEN]";
$query_obj = Bio::DB::Query::GenBank->new(-db    => 'nucleotide',  -query => $query );
 
$gb_obj = Bio::DB::GenBank->new;
 
$stream_obj = $gb_obj->get_Stream_by_query($query_obj);
 
while ($seq_obj = $stream_obj->next_seq) {    
    # do something with the sequence object    
    print $seq_obj->display_id, "\t", $seq_obj->length, "\n";
}


If i cut the 0:3000[SLEN] query it works and returns a lot of sequences, when i alter the query to e.g. 1830[SLEN] it
finds the one sequence that has the length 1830, but i was not able to query a range of lengths.

Please, does anyone know what i am doing wrong.
Greetings
A. Ptok
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