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

Jason Stajich jason at bioperl.org
Mon Sep 15 15:25:49 EDT 2008


Try removing the line
my @ids = $query->ids;

I don't think GenBank supports this part of the query API now or you  
have to execute the query first before you can ask for the number of  
IDs from that object.  I don't remember exactly what changed  
specifically, but I actually get an error with that line:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Id list has been truncated even after maxids requested
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/lib/perl5/Bio/Root/Root.pm:357
STACK: Bio::DB::Query::WebQuery::_fetch_ids /usr/local/lib/perl5/Bio/ 
DB/Query/WebQuery.pm:237
STACK: Bio::DB::Query::WebQuery::ids /usr/local/lib/perl5/Bio/DB/Query/ 
WebQuery.pm:201
STACK: query.pl:9
-----------------------------------------------------------


This is the query script I use that works fine for me for my downloads.

http://fungalgenomes.org/~stajich/scripts/download_query_genbank.pl


I'm using SVN code so it is possible things are changed since 1.5.2.

-jason
On Sep 15, 2008, at 12:05 PM, Andrew Couperthwaite wrote:

> 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
>>
>>
>>
>

Jason Stajich
jason at bioperl.org





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