[Bioperl-l] loading data to biosql tables

[Angshu Kar]

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> 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-
> > 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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>