[Bioperl-l] bioperl-db

[Hilmar Lapp]

I'm not sure what you mean by 'Check interpro.xml', but you can use  
the --safe command-line option to keep going if an individual term  
fails to load for whatever reason.

Can you post the data for the seemingly offending record? (and please  
cc the list)

	-hilmar

On Apr 12, 2008, at 5:39 PM, David Burt wrote:

> Hi Hilmar
>
> Just checked mysql database and only have 39 entries under interpro  
> and loaded up to IPR000035
>
> Check unterpro.xml looks OK from IPR000036 and onwards
>
> So seems to have crashed at IPR000035 ?
>
> dave
>
> 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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