[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 --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


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





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