[Bioperl-l] bioperl-db

Hilmar Lapp hlapp at gmx.net
Sat Apr 12 18:40:53 EDT 2008


Burt - please keep your replies on the list. Others may have input  
too, or benefit from the answer too.

As there is no name() method call on line 914 in the current version  
let's check first that you run a current version of BioPerl. It will  
need to be at least 1.5.2.

However, I do suspect a problem in either the InterPro file itself  
(wouldn't be the first time), or the InterPro parser.

	-hilmar

On Apr 12, 2008, at 5:15 PM, David Burt wrote:

> Hilmar
>
> Many thanks seems to be working
>
> But got this output – any comments/ideas what it means ?
>
> Dave
>
>
> perl load_ontology.pl --host 127.0.0.1 --dbname bioseqdb --dbuser  
> root --dbpass chicken --driver mysql \
> > --namespace "InterPro" --format interprosax interpro.xml
>         ...deleting all relationships for InterPro
>         ...parsing and loading InterPro
> Can't call method "name" on an undefined value at load_ontology.pl  
> line 914.
>
> HERE’S the name and definition in the ontology table
>
> Name = InterPro
>
> Definition =
>
> PANTHER version 6.1, 30128 entries, 04-OCT-2006
> PFAM version 21.0, 8957 entries, 22-NOV-2006
> PIRSF version 2.70, 2877 entries, 12-JUN-2007
> PRINTS version 38.0, 1900 entries, 22-SEP-2005
> PRODOM version 2005.1, 1522 entries, 23-APR-2004
> PROSITE version 20.0, 2006 entries, 14-NOV-2006
> SMART version 5.1, 724 entries, 27-JUL-2007
> TIGRFAMs version 7.0, 3423 entries, 28-SEP-2007
> GENE3D version 3.0.0, 2147 entries, 11-SEP-2006
> SSF version 1.69, 1538 entries, 30-NOV-2006
> SWISSPROT version 55.1, 359942 entries, 18-MAR-2008
> TREMBL version 38.1, 5443281 entries, 18-MAR-2008
> INTERPRO version 17.0, 16175 entries, 19-MAR-2008
> GO version N/A, 23937 entries, 27-MAR-2007
> MEROPS version 7.8, 2831 entries, 12-JUL-2007 |
>
>
>
> From: Hilmar Lapp [mailto:hlapp at gmx.net]
> Sent: 12 April 2008 19:16
> To: David Burt
> Cc: Bioperl BioPerl
> Subject: Re: bioperl-db
>
> Hi Burt,
>
> can you try format interprosax instead of interpro? That variant is  
> also much more graceful regarding required space.
>
>             -hilmar
>
> On Apr 12, 2008, at 1:01 PM, David Burt wrote:
>
>
> Hi Hilmar,
>
> Hope you can help – I am using bioperl-db to create a biosql database
>
> I have used scripts load_seqdatabase.pl and load_ontology.pl to  
> install human swissprot entries, gene ontology, sequence ontology  
> and now want to load interpro
>
> Here’s the command line I have tried
>
> perl load_ontology.pl --host 127.0.0.1 --dbname bioseqdb --dbuser  
> root --dbpass chicken --driver mysql \
> --namespace "InterPro" --format InterPro interpro.xml
>
> But I get this message
>
> Can't call method "identifier" on an undefined value at  /cygdrive/ 
> c/Bioinformatics/Ensembl/src/bioperl-live/Bio/Ontology/ 
> SimpleOntologyEngine.pm line 395
>
> Any ideas?
>
> Dave
>
> PS: here’s the top of the interpro.xml file
>
> <?xml version="1.0" encoding="ISO-8859-1"?>
> <!DOCTYPE interprodb SYSTEM "interpro.dtd">
>
>
>
> <interprodb>
>     <release>
>       <dbinfo dbname="PANTHER" version="6.1" entry_count="30128"  
> file_date="04-OCT-2006 00:00:00" />
>       <dbinfo dbname="PFAM" version="21.0" entry_count="8957"  
> file_date="22-NOV-2006 00:00:00" />
>       <dbinfo dbname="PIRSF" version="2.70" entry_count="2877"  
> file_date="12-JUN-2007 00:00:00" />
>       <dbinfo dbname="PRINTS" version="38.0" entry_count="1900"  
> file_date="22-SEP-2005 00:00:00" />
>       <dbinfo dbname="PRODOM" version="2005.1" entry_count="1522"  
> file_date="23-APR-2004 00:00:00" />
>       <dbinfo dbname="PROSITE" version="20.0" entry_count="2006"  
> file_date="14-NOV-2006 00:00:00" />
>       <dbinfo dbname="SMART" version="5.1" entry_count="724"  
> file_date="27-JUL-2007 00:00:00" />
>       <dbinfo dbname="TIGRFAMs" version="7.0" entry_count="3423"  
> file_date="28-SEP-2007 00:00:00" />
>       <dbinfo dbname="GENE3D" version="3.0.0" entry_count="2147"  
> file_date="11-SEP-2006 00:00:00" />
>       <dbinfo dbname="SSF" version="1.69" entry_count="1538"  
> file_date="30-NOV-2006 00:00:00" />
>       <dbinfo dbname="SWISSPROT" version="55.1"  
> entry_count="359942" file_date="18-MAR-2008 00:00:00" />
>       <dbinfo dbname="TREMBL" version="38.1" entry_count="5443281"  
> file_date="18-MAR-2008 00:00:00" />
>       <dbinfo dbname="INTERPRO" version="17.0" entry_count="16175"  
> file_date="19-MAR-2008 00:00:00" />
>       <dbinfo dbname="GO" version="N/A" entry_count="23937"  
> file_date="27-MAR-2007 00:00:00" />
>       <dbinfo dbname="MEROPS" version="7.8" entry_count="2831"  
> file_date="12-JUL-2007 16:56:17" />
>     </release>
>   <interpro id="IPR000001" type="Domain" short_name="Kringle"  
> protein_count="352">
>     <name>Kringle</name>
>     <abstract>
>
>
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================






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