[Bioperl-l] loading data to biosql tables

[Angshu Kar]

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.
>
> 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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> > > Bioperl-l at portal.open-bio.org
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> >
>
>