[Bioperl-l] bioperl-db

David Burt david at burt7259.freeserve.co.uk
Sun Apr 13 10:32:31 EDT 2008


Hi Hilmar

 

Many thanks for info - tried a few things

 

1. First tried --safe flag

 

perl load_ontology.pl --host 127.0.0.1 --dbname bioseqdb --dbuser root
--dbpass chicken --driver mysql --safe \

 --namespace "InterPro" --format interprosax interpro.xml

 

Still got same output as before

 

        ...deleting all relationships for InterPro

        ...parsing and loading InterPro

 

Can't call method "name" on an undefined value at load_ontology.pl line 914

 

Only 35 interpro entries entered into database

 

2. I am using bioperl 1.5.2

 

3. I downloaded Release 17.0, 20 March 2008 of the interpro.xml file from
ftp://ftp.ebi.ac.uk/pub/databases/interpro/

 

I did not send this file, sine it was ~10Mb gzipped

 

Dave

 

 



More information about the Bioperl-l mailing list