[Bioperl-l] problem with bioperl on UNIX

[simon andrews (BI)]

> -----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.

--
Simon Andrews PhD
Bioinformatics Dept
The Babraham Institute

simon.andrews at bbsrc.ac.uk
+44 (0)1223 496463