[BioPython] problem loading NCBI_taxonomy database into bioseqdb

[Nick Matzke]

Hi all,

I'm following the BioSQL tutorial at the biopython website 
(http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy ).  I can get 
bioseqdb to work, and the biosql python scripts etc.

However I can't get these directions to work in loading the taxonomy 
database into bioseqdb.  I get: "Can't locate object method "connect" 
via package "DBI" "

I double-checked to make sure I've got DBI in perl (see error message 
below) but that doesn't seem to help.

Any help appreciated!
Nick


commands/returns:
===========================
===========================
===========================
mws2:/bioinformatics/eg nick$ perl -v

This is perl, v5.10.0 built for darwin-thread-multi-2level
(with 3 registered patches, see perl -V for more detail)

Copyright 1987-2007, Larry Wall

Binary build 1002 [283697] provided by ActiveState 
http://www.ActiveState.com
Built Jan 10 2008 11:08:33

Perl may be copied only under the terms of either the Artistic License 
or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.






mws2:/bioinformatics/eg nick$ sudo cpan DBI
Password:

CPAN: Storable loaded ok (v2.18)
Going to read /usr/local/Metadata
   Database was generated on Wed, 23 Jul 2008 10:02:50 GMT
CPAN: LWP::UserAgent loaded ok (v5.810)
CPAN: Time::HiRes loaded ok (v1.9711)
Fetching with LWP:
   http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz
CPAN: YAML loaded ok (v0.66)
Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz
............................................................................DONE
Fetching with LWP:
   http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz
Going to read /Users/nick/.cpan/sources/modules/02packages.details.txt.gz
   Database was generated on Mon, 01 Sep 2008 10:02:51 GMT
............................................................................DONE
Fetching with LWP:
   http://ppm.activestate.com/CPAN/modules/03modlist.data.gz
Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz
............................................................................DONE
Going to write /usr/local/Metadata
DBI is up to date (1.607).






mws2:/bioinformatics/eg nick$ 
/bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl 
--dbname bioseqdb --driver mysql --dbuser root --download true


Can't locate object method "connect" via package "DBI" at 
/bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl 
line 323.

mws2:/bioinformatics/eg nick$
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-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab websites:
http://ib.berkeley.edu/people/lab_detail.php?lab=54
http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page: 
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology
VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week)

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
====================================================