[Bioperl-l] problem with bioperl on UNIX

[Prachi Shah]

Thanks Simon and Matthew for your tips. dos2unix did
not make a difference. I am using perl 5.6.0 with
bioperl 1.2, so its the latest. No proxy on the
machine and the strange thing is.....when I use LWP
useragent directly to connect to NCBI Entrez, it
works. But with Bio::DB::Query::GenBank it still gives
me the 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.

Any more ideas are very welcome...
Thanks,
Prachi.

# In case you need the code....see at the end.

--- "simon andrews (BI)" <simon.andrews at bbsrc.ac.uk>
wrote:
> 
> > -----Original Message-----
> > From: Prachi Shah 
> > Subject: [Bioperl-l] problem with bioperl on UNIX
> > 
> > It works perfectly fine on the Win perl setup,
> > but when I use it on the UNIX system it gives me
> the
> > following error:
> > 
> 
> I just ran your code directly on our system, and it
> worked fine; not so much as a warning.  This was
> using BioPerl 1.2 under Linux, Perl 5.6.0.
> 
> It looks as though your query setup is going wrong. 
> Your first error:
> 
> > Use of uninitialized value in concatenation (.) at
> > tryBioPerl.pl line 18.
> 
> ..comes from $count being undef, which means that
> the $query->count didn't return anything.  The call
> to Bio::DB::Query must have worked though otherwise
> you'd have got a warning saying "can't call count on
> an undefined value", so your problem is that your
> query worked, but no hits were returned.  There are
> a couple of potential reasons for this;
> 
> 1) Genbank wasn't working properly when you tried
> it.  Try it again and see if it works now!
> 
> 2) Your network setup on your unix box isn't
> allowing you to connect to the genbank site
> properly.  This is usually because your connection
> must pass through a proxy server to access the
> internet, and you haven't given Perl the details of
> this proxy.  The easiest way to do this is to set
> the 'http_proxy' environment variable in your shell
> (or within your script using the %ENV hash).
> 
> $ENV{'http_proxy'}='http://my.proxy.address:port';
> 
> You might also want to try upgrading your BioPerl to
> the latest version in case you are hitting a problem
> with an older version.
> 
> Hope this helps
> 
> Simon.



###### 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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