[Bioperl-l] problem with bioperl on UNIX

[Hilmar Lapp]

my $query = Bio::DB::Query::GenBank->new(-verbose => 1, ....);

Every bioperl object accepts -verbose => <some number> for the 
constructor.

	-hilmar

On Thursday, February 6, 2003, at 03:07  PM, Prachi Shah wrote:

> I am sorry, this might be silly......but what
> initialization should I add "-verbose=>1" ?
>
> --- Jason Stajich <jason at cgt.mc.duke.edu> wrote:
>> add -verbose => 1
>> to your initialization.
>>
>>
>> On Thu, 6 Feb 2003, Prachi Shah wrote:
>>
>>> Hmmm....
>>> Well, it never works for me. Is there a way to
>> view
>>> detailed error/rejection message received from
>>> GenBank? That might give a better idea of what is
>>> actually happening. All the error that I see right
>> now
>>> tells me that for some reason no results were
>>> returned. But, knowing that reason might really
>> help.
>>>
>>> thanks,
>>> Prachi.
>>>
>>>
>>> --- Jason Stajich <jason at cgt.mc.duke.edu> wrote:
>>>> It is possible genbank is/was rejecting queries
>> - I
>>>> am able to execute
>>>> your query on a linux box.  I had trouble
>> yesterday
>>>> trying to run your
>>>> code though.  It is possible that GenBank was
>> having
>>>> problems when you
>>>> last tried to execute your code.
>>>>
>>>> #!/usr/bin/perl -w
>>>> use strict;
>>>> use Bio::DB::Query::GenBank;
>>>>
>>>> my $query_string = 'Gallus gallus[organism]';
>>>>
>>>> my $query = Bio::DB::Query::GenBank->new(-db
>> =>
>>>> 'protein',
>>>> 				      -query=>$query_string);
>>>> my $count = $query->count;
>>>> print "COUNT is $count\n";
>>>>
>>>> I get:
>>>>
>>>> COUNT is 7742
>>>>
>>>>
>>>> -jason
>>>>
>>>
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>>
>> --
>> Jason Stajich
>> Duke University
>> jason at cgt.mc.duke.edu
>
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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