[Bioperl-l] loading data to biosql tables
Angshu Kar
angshu96 at gmail.com
Sat Dec 10 21:51:53 EST 2005
Oh...may be u missed my last mail... I'm sedning it again...
Now I'm getting this new error:
Can't locate Bio/DB/BioDB.pm in @INC (@INC contains:
/home/akar/local/perl//i386-linux-thread-multi /home/akar/local/perl/
/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 8.
BEGIN failed--compilation aborted at load_seqdatabase.pl line 8.
I've checked the Bio/DB/ folder but it doesn't contain the BioDB.pm module -
it contains the following:
Ace.pm <http://ace.pm/> DBFetch.pm Flat GFF
MeSH.pm RefSeq.pm Taxonomy.pm <http://taxonomy.pm/>
XEMBLService.pm
Biblio EMBL.pm Flat.pm <http://flat.pm/> GFF.pm
NCBIHelper.pm Registry.pm <http://registry.pm/>
Universal.pm<http://universal.pm/>
BiblioI.pm Failover.pm <http://failover.pm/> GDB.pm
InMemoryCache.pm Query SeqI.pm UpdateableSeqI.pm
BioFetch.pm Fasta.pm <http://fasta.pm/> GenBank.pm Makefile.PL
QueryI.pm SwissProt.pm WebDBSeqI.pm
CUTG.pm FileCache.pm GenPept.pm MANIFEST RandomAccessI.pm
Taxonomy XEMBL.pm
Have I installed some wrong version of bioperl-db ? (I've used
http://bio.perl.org/Core/Latest/index.shtml)<http://bio.perl.org/Core/Latest/index.shtml%29>
Thanks,
Angshu
On 12/10/05, Hilmar Lapp <hlapp at gmx.net> wrote:
>
>
> On Dec 10, 2005, at 6:38 PM, Angshu Kar wrote:
>
> > Hi Hilmar,
> >
> > I've run the biosqldb-pg.sql through psql successfully. It has created
> > 28 tables. :(
>
> That sounds good. Why are you unhappy about it?
>
> > Are there any other possibilities?
>
> To achieve what?
>
> -hilmar
>
> >
> > Thanks,
> > Angshu
> >
> >
> > On 12/10/05, Hilmar Lapp <hlapp at gmx.net> wrote:You should download the
> > current biosql-schema from CVS. If my
> >> recollection is correct then you are on Postgres, so you will want to
> >> run the file biosqldb-pg.sql through psql. You do not need the other
> >> Postgres related files there. The rest of the repository, aside from
> >> support for other RDBMSs (mysql, Oracle, and HSQL), contains
> >> documentation, an ERD of the schema, and the script for loading the
> >> NCBI taxonomy database.
> >>
> >> -hilmar
> >>
> >> On Dec 9, 2005, at 1:58 PM, Angshu Kar wrote:
> >>
> >> > Hi Hilmar,
> >> >
> >> > I'm obliged that you showed me the light. I reanalyzed the schema
> >> and
> >> > found that its no use working with a truncated version of
> >> > biosql-schema and now I'm planning to install the entire schema.
> >> Could
> >> > you please let me know where can I find the script for that for a Pg
> >> > db?
> >> >
> >> > Thank you so much. Else I would have to face a lots of problem in
> >> the
> >> > later half of my project.
> >> >
> >> > Gratefully,
> >> > Angshu
> >> >
> >> > On 12/9/05, Hilmar Lapp <hlapp at gmx.net> wrote:Angshu,
> >> > load_seqdatabase.pl is a script that utilizes the language
> >> >> binding library bioperl-db to load sequences and annotation into
> >> >> Biosql. The object-relational mapping code is all over bioperl-db.
> >> >>
> >> >> I'm sorry, but if you believe it is worth fiddling with that
> >> >> object-relational code to 'save' instantiating a few more tables
> >> then
> >> >> you're welcome to do so but you're essentially on your own.
> >> >>
> >> >> Also, if you'd like to work with a schema the language binding of
> >> >> which
> >> >> allows to arbitrarily drop tables from the schema and still work
> >> then
> >> >> Biosql/bioperl-db may not be for you.
> >> >>
> >> >> -hilmar
> >> >>
> >> >> On Dec 9, 2005, at 7:10 AM, Angshu Kar wrote:
> >> >>
> >> >> > Hi Hilmar,
> >> >> >
> >> >> > In the load_seqdatabase.pl script could you please tell me where
> >> you
> >> >> > are inserting the data into the db tables, so that I can try and
> >> >> > modify that part to insert data only to the tables that I need ?
> >> >> >
> >> >> > Thanks,
> >> >> > Angshu
> >> >> >
> >> >> >
> >> >> > On 12/8/05, Hilmar Lapp <hlapp at gmx.net > wrote: Any reason you
> >> didn't
> >> >> > instantiate the rest of the schema? Any scripts
> >> >> >> and software that have been written against BioSQL will
> >> certainly
> >> >> >> expect the rest of the schema be present ...
> >> >> >>
> >> >> >> Bioperl-db is the BioSQL language binding for Bioperl, so that's
> >> >> what
> >> >> >> you will want to use. It comes with a script
> >> load_seqdatabase.pl to
> >> >> >> load any format supported by Bioperl.
> >> >> >>
> >> >> >> However, bioperl-db does expect all of Biosql to be present ...
> >> >>>>
> >> >> >> -hilmar
> >> >> >>
> >> >> >> On Dec 7, 2005, at 6:12 PM, Angshu Kar wrote:
> >> >> >>
> >> >> >> > Hi,
> >> >> >> >
> >> >> >> > I've created 5 tables (taxon, taxon name, bioentry,
> >> biosequence,
> >> >> >> > biodatabase) in my postgresql database (linux box) using the
> >> >> biosql
> >> >> >> > schema
> >> >> >> > ddl from
> >> >> >> >
> >> >> >>
> >> http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/
> >> >> >> sql/
> >> >> >> >
> >> >> >> biosqldb-pg.sql?rev=1.29&cvsroot=biosql&content-type=text/
> >> >> >> vnd.viewcvs-
> >> >> >> > markup
> >> >> >> >.
> >> >> >> > Now I want to load the tables with arabidopsis data. Could you
> >> >> >> please
> >> >> >> > let me
> >> >> >> > know where can I find such scripts for pgsql? And also I find
> >> at
> >> >> >> > http://bio.perl.org/Core/Latest/index.shtml that the DB module
> >> >> has
> >> >> >> not
> >> >> >> > been
> >> >> >> > updated since 2001. Do I need to install that? Or are there
> >> some
> >> >> new
> >> >> >> > releases?
> >> >> >> >
> >> >> >> > I'll be obliged if you can guide.
> >> >> >> >
> >> >> >> > Thanks,
> >> >> >> > Angshu
> >> >> >> >
> >> >> >> > _______________________________________________
> >> >> >> > Bioperl-l mailing list
> >> >> >> > Bioperl-l at portal.open-bio.org
> >> >> >> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >> >> >> >
> >> >> >> >
> >> >> >> --
> >> >> >> -------------------------------------------------------------
> >> >> >> Hilmar Lappemail: lapp at gnf.org
> >> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> >> >> -------------------------------------------------------------
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> --
> >> >> -------------------------------------------------------------
> >> >> Hilmar Lappemail: lapp at gnf.org
> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> >> -------------------------------------------------------------
> >> >>
> >> >>
> >> >>
> >> --
> >> -------------------------------------------------------------
> >> Hilmar Lappemail: lapp at gnf.org
> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> -------------------------------------------------------------
> >>
> >>
> >>
> --
> -------------------------------------------------------------
> Hilmar Lapp email: lapp at gnf.org
> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>
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