[Bioperl-l] struggling with Bio::Index::GenBank

[Neil Saunders]

I hope this is not too basic a question, but I am struggling.  I have
downloaded the gbbct subset of GenBank and want to index it.  I run
BioPerl 1.2 on Debian/Linux and have all the dependencies installed
(Berkeley DB, the DB_File module and most Debian packages related to
Berkeley dbm (e.g. libdb3-dev and libberkeleydb-perl).

I'm just using the code example that comes with Bio::Index::GenBank and
my file is /usr/local/databases/gbbct.seq, so I run:

make_index.pl /usr/local/databases/gbbct.seq

but persistently get the error:

------------- EXCEPTION  -------------
MSG: Can't open 'DB_File' dbm file '/usr/local/databases/gbbct.seq' :
File exists
STACK Bio::Index::Abstract::open_dbm
/usr/local/share/perl/5.6.1/Bio/Index/Abstract.pm:389
STACK Bio::Index::Abstract::new
/usr/local/share/perl/5.6.1/Bio/Index/Abstract.pm:150
STACK Bio::Index::AbstractSeq::new
/usr/local/share/perl/5.6.1/Bio/Index/AbstractSeq.pm:91
STACK toplevel ./index_gb.pl:9


As I'm not that clear on the workings of the index module, I find this
confusing.  Am I obviously doing something wrong or missing something?

Neil
-- 
 School of Biotechnology and Biomolecular Sciences,
 The University of New South Wales,
 Sydney 2052,
 Australia

http://psychro.bioinformatics.unsw.edu.au/neil/index.php