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

Mike Muratet muratem at eng.uah.edu
Tue Mar 21 17:03:30 EST 2006



On Tue, 21 Mar 2006, Brian Osborne wrote:

> Mike,
>
> Are you sure that the "location" and "dbname" are right? Usually these will
> be different - from the OBDA HOWTO:
>
> Once the flat database is created you can configure your seqdatabase.ini
> file. Let's say that you have used the bioflat_index.pl script to create
> the flat database and a new directory called ppp has been created in your
> /home/sally/bioinf/ directory (and the ppp/ directory contains the
> config.dat file).
>
> This refers to this Registry entry:
>
> protocol=flat
> location=/home/sally/bioinf
> dbname=ppp
>
> Perhaps the location should be "/opt/muratet"? You may have to change
> OBDA_LOCATION as well.
>
> Brian O.

Brian

Thanks, I think I've got it sorted out now. I changed things around to 
be closer to the situation in the 
HOWTO. I changed the root to /opt/mmuratet and the dbname to harry. I 
reran bp_bioflatindex.pl with the new parameters and changed 
seqdatabase.ini to:

VERSION=1.00

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

It created a new directory, harry, under the root /opt/mmuratet which has 
the appropriate entries. I set OBDA_LOCATION=/opt/mmuratet. Then I changed 
the command,

bp_biogetseq.pl --dbname fungal_genomes etc etc

and it works.

Thanks for the help.

Mike
>
>
> On 3/21/06 12:09 PM, "Mike Muratet" <muratem at eng.uah.edu> wrote:
>
>> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>


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