oracular (3) Bio::DB::QueryI.3pm.gz

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