[Bioperl-l] Reconstructing BLAST output

[Will Spooner]

The way that the Ensembl system works is as follows;

- Run the search (Bio::Tools::Run::Search, not yet in BioPerl),
- Parse the report (Bio::SearchIO),
- Save the parsed Bio::Search::Result objects to a MySQL database.

For the final step I needed to;

- Write a Bio::Root::Storable class that provides inheritable methods for 
  serialising BioPerl objects. This is in BioPerl, but an updated version 
  will be added,

- Create a Bio::Search::Result::StorableResult that inherets Storable,
  and similar modules for Hit and HSP,

- Write a Bio::Root::Storable compliant adaptor to connect to the MySQL 
  database.


Implementation code looks a bit like this;

  # Storing
  my $adaptor = Bio::EnsEMBL::External::BlastAdaptor->new( @args );
  my $result  = $searchio->next_result();
  my $ticket  = $result->store( $adaptor );
  ...
  # Retrieving
  my $result = Bio::Root::Storable->retrieve( $ticket, $adaptor );


For different schemas you would simply need a customised adaptor module. 
Does this tie in with your ideas Jason?

All the code is in Ensembl/BioPerl CVS. An overview document is available 
from;
  http://www.ensembl.org/Docs/linked_docs/BlastView_search_api.pdf
  (caveat - quite old, some differences from current system)


Will

On Thu, 28 Oct 2004, Jason Stajich wrote:

> See Bio::SearchIO::Writer::TextResultWriter and HTMLResultWriter which 
> reconstitute a report based on Bio::Search objects.  You will need to 
> build Bio::Search objects however from the DB - something that I am 
> sure has been done in part somewhere already.  Ensembl also has their 
> own way to store this data but I don't think are using Bio::Search type 
> object for it at the moment.
> 
> If someone gets this bit of to-from RDMBS code working for would be 
> really nice to have it in bioperl as just a simple component.   I know 
> lots of people have their own store-similarity-search-results schemas 
> out there, happy to see a Bio::Search serializiation layer written to 
> talk to these.
> 
> -jason
> On Oct 28, 2004, at 11:36 AM, Adam Woolfe wrote:
> 
> > Hi,
> >
> > I was just wondering if there was any module in bioperl that can
> > reconstruct BLAST output from the constituent data. I have parsed BLAST
> > output using SeqIO into a relational database (so I have all the
> > constituent data), but now i need to print
> > that data back out to look like BLAST output. I know it sounds crazy 
> > but
> > thats what i need.
> >
> > cheers
> >
> > adam
> >
> > _______________________________________________
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> >
> >
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
> 
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