[Bioperl-l] Bio::DB::Query::GenBank question

Andrew Couperthwaite acouperthwaite at gmail.com
Mon Sep 15 15:05:13 EDT 2008


the code i'm starting with is this:
=====
use Bio::DB::Query::GenBank;
use Bio::DB::GenBank

my $query_string = 'Oryza[Organism] AND EST[Keyword]';
    my $query = Bio::DB::Query::GenBank->new(-query =>  
'Oryza[Organism] AND EST[Keyword]',
    											-db=>'nucleotide');
    my $count = $query->count;
    my @ids   = $query->ids;
    # get a genbank database handle
    my $gb = Bio::DB::GenBank->new();
    my $stream = $gb->get_Stream_by_query($query);

    while (my $seq = $stream->next_seq) {
       # do something with the sequence object
       print "hello";
    }
=====
It doesn't produce any error messages, it simply doesn't enter the  
while loop.  It seems as though it isn't getting any results from  
genbank?/isn't contacting genbank?

We are running version 1.5.2.  Haven't updated since late May.

-Andrew

On 13-Sep-08, at 12:42 AM, Jason Stajich wrote:

> Hi Andrew -
>
> a) what is the exact script code you are trying, what are the error  
> messages?
> b) what version of bioperl?
>
> The first thing we'll suggest is: did you get the latest code from  
> SVN yet or a nightly build?
>
> -jason
> On Sep 12, 2008, at 2:17 PM, Andrew Couperthwaite wrote:
>
>> Hi,
>>
>> I'm having difficulty using  the Bio::DB::Query::GenBank module.   
>> The sample script on the page http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Query/GenBank.html 
>>  doesn't seem to work.
>>
>> I'm trying to use this and the Bio::DB::GenBank module to find and  
>> download a set of sequences from GenBank...
>> I'm rather new to bioperl, can anyone point me in the right  
>> direction?
>>
>> Thanks,
>> -Andrew
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Jason Stajich
> jason at bioperl.org
>
>
>



More information about the Bioperl-l mailing list