[Bioperl-l] problem with bioperl on UNIX

[Prachi Shah]

Hi,

I had to switch from Win32 system to UNIX systems and
I was also trying to use BioPerl. Below is a simple
script which some of you have seen a couple of days
back. It works perfectly fine on the Win perl setup,
but when I use it on the UNIX system it gives me the
following error:

Use of uninitialized value in concatenation (.) at
tryBioPerl.pl line 18.
COUNT 
Can't use an undefined value as an ARRAY reference at
/home/pss11/Perl/bioperl-1.2/lib/site_perl/5.6.0/Bio/DB/Query/WebQuery.pm
line 204.

The only change is the 'use lib' statement which I had
to use because I do not have root permissions on the
UNIX machine. Any ideas on this??

thanks,
Prachi.


###### code starts here ####

#! /usr/bin/perl -w

use lib qw(
/home/pss11/Perl/bioperl-1.2/lib/site_perl/5.6.0
/home/pss11/Perl/IO-String-1.02/lib/site_perl/5.6.0
/home/pss11/Perl/libwww-perl-5.69/lib/site_perl/5.6.0
/home/pss11/Perl/URI-1.23/lib/site_perl/5.6.0);

use IO::String;
use strict;
use Bio::DB::GenBank;
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 $count\n";

my @ids   = $query->ids;

open(OUT,">/home/pss11/AutoBlast-GI-UNIX/queryout");

while(@ids)
{
        my $prt = shift @ids;
        print OUT "$prt \n";
}
close(OUT);



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