[Bioperl-l] problem with Bio::DB::Query::GenBank

[Brian Osborne]

Prachi,

You want to say:

use Bio::DB::Query::GenBank;

Not "use Bio::Perl".

But your script reveals a documentation error in the module. The module says

$query->get_Ids

but that won't work, it should say

$query->ids

I'll fix that...


Brian O.


-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Prachi Shah
Sent: Thursday, January 30, 2003 1:12 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] problem with Bio::DB::Query::GenBank


Hi Everyone!

I just started using it and my first little 'Hello
world' quality script failed with the following error:


Can't locate object method "new" via package
"Bio::DB::Query::GenBank" (perhaps you forgot to load
"Bio::DB::Query::GenBank"?) at C:\tryBioPerl.pl line
5.

I checked the GenBank.pm and the code looks ok. And of
course, I did not forget to load
"Bio::DB::Query::GenBank". I am using Active state
Perl 5.6.1 for Win32 and BioPerl 1.2 on Windows 2000
system.
Any ideas on this are greatly appreciated.

Thanks,
Prachi.

##### Code starts here. #####

#! perl -w

use strict;
use Bio::Perl;

my $query_string = 'Gallus gallus[Organism] AND ATP';
my $query =
Bio::DB::Query::GenBank->new(-db=>'nucleotide',
  -query=>$query_string);
my $count = $query->count;
my @ids   = $query->get_Ids;

print "COUNT $count\n";
print " IDS \n @ids";



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