[Bioperl-l] loading data to biosql tables

[Barry Moore]

Angshu-

 

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'.

 

Barry

 

 

 

 

-----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 <mailto: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.

Thanks,
Angshu

 

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

Angshu-

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.

Barry

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto: bioperl-l-
<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
downloaded
> my
> datafile which is ATH1_cds_cm_20040228 from TAIR. What's the namespace

and
> format for this?
>
> Thanks,
> Angshu
>
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