FW: [Bioperl-l] loading data to biosql tables

Barry Moore bmoore at genetics.utah.edu
Mon Dec 12 13:53:10 EST 2005

I support Hilmar's previous post about "Newbie's".  This is the kind of question that you should be able to answer for yourself with a some effort on your part.
From: Angshu Kar [mailto:angshu96 at gmail.com] 
Sent: Sunday, December 11, 2005 8:59 AM
To: Barry Moore
Subject: Re: [Bioperl-l] loading data to biosql tables
But Barry my problem is that despite installing bioperl and bioperl-db module I cannot find the BioDB.pm.
Did I install anything wrong?

On 12/11/05, Barry Moore <bmoore at genetics.utah.edu> wrote: 
You can either add: 'use lib /path/to/your/Root.pm;' at the top of all of your perl scripts, or set PERL5LIB to the path of your Root.pm.  For example, I use the bash shell, and in my .bashrc file I have a line 'export PERL5LIB=/home/bmoore/perl/lib'. 
-----Original Message-----
From: Angshu Kar [mailto: angshu96 at gmail.com] 
Sent: Friday, December 09, 2005 5:55 PM
To: Barry Moore
Cc: bioperl-l
Subject: Re: [Bioperl-l] loading data to biosql tables
One thing I missed was that my Root.pm resides in a different path...How to specify that?
On 12/9/05, Angshu Kar < angshu96 at gmail.com> wrote:
Thanks a lot Barry.

Now I'm getting this error while tryin to run the load_seqdatabase.pl in a linux box (I used : 
perl load_seqdatabase.pl /akar/seq/ATH1_cds_cm_20040228)

Can't locate Bio/Root/Root.pm in @INC (@INC contains: /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at load_seqdatabase.pl line 7. 
BEGIN failed--compilation aborted at load_seqdatabase.pl line 7.

Please guide.

On 12/9/05, Barry Moore < bmoore at genetics.utah.edu> wrote:

Make the namespace whatever you want it to be.  This is useful if you 
want to load sequence from different sources into the same database.  As 
for the format - you tell us what format is the file in?  You could just
let bioperl guess, but looking at the file and deciding yourself would 
be your best bet.


> -----Original Message----- 
> From: bioperl-l-bounces at portal.open-bio.org [mailto: bioperl-l-
> bounces at portal.open-bio.org] On Behalf Of Angshu Kar
> Sent: Friday, December 09, 2005 5:22 PM 
> To: Sean Davis
> Cc: bioperl-l
> Subject: Re: [Bioperl-l] loading data to biosql tables
> Hi Sean,
> A small help I need before I run the load_seqdatabase.pl. I've
> my
> datafile which is ATH1_cds_cm_20040228 from TAIR. What's the namespace 
> format for this?
> Thanks,
> Angshu
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> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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