NAME

Bio::DB::QueryI - Object Interface to queryable sequence databases

SYNOPSIS

   # using Bio::DB::Query::GenBank as an example
   my $query_string = 'Oryza[Organism] AND EST[Keyword]';
   my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide',
                                            -query=>$query_string);
   my $count = $query->count;
   my @ids   = $query->ids;

   # get a genbank database handle
   $gb = Bio::DB::GenBank->new();
   my $stream = $db->get_Stream_by_query($query);
   while (my $seq = $stream->next_seq) {
      ...
   }

   # initialize the list yourself
   my $query = Bio::DB::Query::GenBank->new(-ids=>['X1012','CA12345']);

DESCRIPTION

This interface provides facilities for managing sequence queries such as those offered by Entrez. A query object is created by calling new() with a database-specific argument list. From the query object you can either obtain the list of IDs returned by the query, or a count of entries that would be returned. You can pass the query object to a Bio::DB::RandomAccessI object to return the entries themselves as a list or a stream.

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@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Lincoln Stein

Email lstein@cshl.org

APPENDIX

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

new

 Title   : new
 Usage   : $db = Bio::DB::QueryI->new(@args);
 Function: constructor
 Returns : QueryI object
 Args    : -query       a query string
           -ids         a list of ids as an arrayref

Create new QueryI object. You may initialize with either a query string or with a list of ids. If both ids and a query are provided, the former takes precedence.

Subclasses may recognize additional arguments.

count

 Title   : count
 Usage   : $count = $db->count;
 Function: return count of number of entries retrieved by query
 Returns : integer
 Args    : none

Returns the number of entries that are matched by the query.

ids

 Title   : ids
 Usage   : @ids = $db->ids([@ids])
 Function: get/set matching ids
 Returns : array of sequence ids
 Args    : (optional) array ref with new set of ids

query

 Title   : query
 Usage   : $query = $db->query([$query])
 Function: get/set query string
 Returns : string
 Args    : (optional) new query string