[Bioperl-l] bp_genbank2gff problems

[Neil Saunders]

I'm having a frustating time with the bp_genbank2gff.pl script.

I have 2 systems:

(1) Debian sid, perl 5.8.2, latest CVS bioperl-live, bioperl-run and
Gbrowse.
(2) Debian woody, perl 5.6.1, CVS versions as above.

I have written a script that takes a set of GenBank files and pipes
them through various processes to generate GFF, Fasta and conf files
for use with Gbrowse.  On system (1) above, I use:

bp_genbank2gff.pl -file <file> -stdout

No problems, GFF3 file output appears.

On system (2) above, the same command gives errors of the type:

------------- EXCEPTION  -------------
MSG: Can't connect to database: Access denied for user: '@localhost' to
database 'test'
STACK Bio::DB::GFF::Adaptor::dbi::caching_handle::new
/usr/local/share/perl/5.6.1/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm:89
STACK Bio::DB::GFF::Adaptor::dbi::new
/usr/local/share/perl/5.6.1/Bio/DB/GFF/Adaptor/dbi.pm:93
STACK Bio::DB::GFF::Adaptor::dbi::mysql::new
/usr/local/share/perl/5.6.1/Bio/DB/GFF/Adaptor/dbi/mysql.pm:270
STACK Bio::DB::GFF::Adaptor::biofetch::new
/usr/local/share/perl/5.6.1/Bio/DB/GFF/Adaptor/biofetch.pm:95
STACK Bio::DB::GFF::new /usr/local/share/perl/5.6.1/Bio/DB/GFF.pm:599
STACK toplevel /home/neil/gbrowse/genomes/scripts/bp_genbank2gff.pl:218

--------------------------------------
DBI->connect(test) failed: Access denied for user: '@localhost' to
database 'test' at
/usr/local/share/perl/5.6.1/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
line 139


Clearly the bp_genbank2gff script is trying to access a database 'test'
on 'localhost' with no user.  I guess my question is: why?  I have told
it to send to stdout.  As I have the same bioperl version on both
machines, I'm pretty confused.  The only thing I noticed from 'make
test' on the woody machine was this failure:

t/GFF.t       255 65280    32   24  75.00%  21-32

Relevant?

thanks for any pointers,

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