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

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


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    :



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