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

Mike Muratet muratem at eng.uah.edu
Tue Mar 21 16:39:48 EST 2006



On Tue, 21 Mar 2006, khoueiry wrote:

> hi Mike,
>
> If I well understood your question, you want to index a fasta file to
> fetch it. For that puropose, I already wrote a perl scirpt to do that
> (view attachment). It is a very simple script, run it without any
> parameters to get a description on the fine way to use it. This file
> will create an index file that you can fetch it:
>
> e. g; once you create your index file (myfile.idx) by the attached
> script, you can fetch any sequence(id) by :
>
> my $indexFile = Bio::Index::Fasta->new(myfile.idx);
> my $seq = $indexFile->fetch(id);
>
> Hope this help
>
> Pierre
>

Pierre

Thanks for the script, I appreciate it. I was (am) trying to get the OBDA 
Bio::Registry to work for the platform independance it provides. I have 
had good success with biosql & load_seqdatabase, too, which you might want 
to try. You generally have to write a little module from the SeqProcessor 
class to handle FASTA IDs, but it's really nice to have things in mySQL.

Cheers

Mike


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