[Bioperl-l] Bio::Registry & Bio::DB::Flat

Mike Muratet muratem at eng.uah.edu
Tue Mar 21 12:09:05 EST 2006


Greetings

I am trying to get index/fetch some fasta files with Bio::Registry and 
Bio::DB::Flat. I created a seqdatabase.ini in $HOME/.bioinformatics 
containing:

VERSION=1.00

[fungal_genomes]
protocol=flat
location=/opt/mmuratet/fungal_genomes
dbname=fungal_genomes

I used the release script bp_bioflat_index.pl to index the files in 
/opt/mmuratet/fungal_genomes and there is a binary key_acc file and a 
config file whose first few lines are:

index   BerkeleyDB/1
format  URN:LSID:open-bio.org:fasta/dna
fileid_11 
/opt/mmuratet/fungal_genomes/fusarium_verticillioides_2.fasta   42688995

I couldn't get my own script to work, so I tried the bp_biogetseq.pl 
script:

bp_biogetseq.pl --dbname fungal_genomes --format fasta \
--namespace acc 'Aspergillus nidulans supercontig 1.5'

-------------------- WARNING ---------------------
MSG: Couldn't call new_from_registry on [Bio::DB::Flat]

------------- EXCEPTION  -------------
MSG: you must specify an indexing scheme
STACK Bio::DB::Flat::new /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Flat.pm:163
STACK Bio::DB::Flat::new_from_registry 
/usr/lib/perl5/site_perl/5.8.5/Bio/DB/Flat.pm:255
STACK (eval) /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Registry.pm:183
STACK Bio::DB::Registry::_load_registry 
/usr/lib/perl5/site_perl/5.8.5/Bio/DB/Registry.pm:182
STACK Bio::DB::Registry::new 
/usr/lib/perl5/site_perl/5.8.5/Bio/DB/Registry.pm:95
STACK toplevel /usr/bin/bp_biogetseq.pl:28

--------------------------------------

---------------------------------------------------
Could not find sequence with identifier [Aspergillus nidulans supercontig 
1.5]

Can anyone see anything I've done wrong? It all seems in agreement with 
the documentation. I found a few old threads but I can't see where it ever 
got resolved. I have set the environment variables OBDA_INDEX=bdb and 
OBDA_LOCATION=/opt/mmuratet/fungal_genomes.

Thanks

Mike


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