NAME

Bio::DB::SQL::SeqAdaptor - DESCRIPTION of Object

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the object here

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bio.perl.org

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

Describe contact details here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

fetch_by_dbID

 Title   : fetch_by_dbID
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

fetch_by_db_and_accession

 Title   : fetch_by_db_and_accession
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

fetch_by_query

 Title   : fetch_by_query
 Usage   : @seqs = $seqadp->fetch_by_query($bioquery);
 Function:
 Example : @seqs = 
            $seqadp->fetch_by_query(-constraints=>
              ["or",
                   ["and",
                         "species=Human",
                         "keywords=transcription*"],
                   ["and",
                         "species like Drosophila*",
                         "description like *integrase*"],
               ]);
 Returns : list of Bio::Seq objects
 Args    : BioQuery object OR hash reference

Takes a Bio::DB::SQL::BioQuery object, or arguments that can be used to construct one. Right now only the constraints/where part is respected.

Executes the BioQuery by turning the query into individual SqlQuerys (although we could have non-sql adaptors conforming to the same interface as this one, and have the BioQuery translated in some other way)

the BioQuery is a schema independent repesentation of a query; it may or may not be tied to the bioperl object model.

These are the constraint elements that are currently accepted:

(THESE ARE SUBJECT TO CHANGE)

species

This can either by a Bio::Species object, or an NCBI taxonomy ID, or a common_name for the species

references

A string

keywords

A string

description

A string

For all the above constraints, specifying the wildcard character * in the string will automatically make the query use pattern matching (replacing * for % in the sql query, and use the like operand) rather than exact matches.

eg to query by species

    $bioquery = Bio::DB::SQL::BioQuery->new();
    $qc = Bio::DB::SQL::QueryConstraint->new(-name=>"species",
                                             -value=>$species);
    $bioquery->where($qc);
    @seqs=$seqadp->fetch_by_query($bioquery);

or simply

    @seqs=$seqadp->fetch_by_query(-constraints=>"species = $species");

at some point we may want to make the BioQuerys more sql-like, by allowing constraints by Class+attribute like this:

  @seqs=$seqadp->fetch_by_query(-constraints=>"Species.common_name = Human");
  @seqs=$seqadp->fetch_by_query(-constraints=>"Reference.authors = *Shuggy*");

perhaps eventually this method will become private/hidden, and bioperl-db API users will simply do this:

  ($id, $residues) = 
     $bioquery_resolver->do(q[FETCH Seq.primary_seq.display_id, 
                                    Seq.primary_seq.seq 
                              FROM Seq 
                              WHERE Seq.species.ncbi_taxa_id=7227]);

store

 Title   : store
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

remove_by_dbID

 Title   : remove
 Usage   : $seq_adaptor->remove_by_dbID($db_id) or $seq_adaptor->remove_by_dbID(@db_ids)
 Function: removes sequence(s) by their database IDs
 Example :
 Returns : 
 Args    :

get_dates

 Title   : get_dates
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

get_taxa_id

 Title   : get_taxa_id
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

get_keywords

 Title   : get_keywords
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

cpanm Bio::DB::Seq

perl -MCPAN -e shell
install Bio::DB::Seq