Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::DB::Query::GenBank - Build a GenBank Entrez Query

SYNOPSIS

          use Bio::DB::Query::GenBank;
          use Bio::DB::GenBank;

          my $query_string = 'Oryza[Organism] AND EST[Keyword]';
          my $query = Bio::DB::Query::GenBank->new(-db => 'nucleotide',
                                                   -query => $query_string,
                                                   -mindate => '2001',
                                                   -maxdate => '2002');

          print $query->count,"\n";

          # get a Genbank database handle
          my $gb = Bio::DB::GenBank->new();
          my $stream = $gb->get_Stream_by_query($query);
          while (my $seq = $stream->next_seq) {
             # do something with the sequence object
          }

          # initialize the list yourself
          my $query = Bio::DB::Query::GenBank->new(-ids=>[195052,2981014,11127914]);

DESCRIPTION

       This class encapsulates NCBI Entrez queries.  It can be used to store a list of GI
       numbers, to translate an Entrez query expression into a list of GI numbers, or to count
       the number of terms that would be returned by a query.  Once created, the query object can
       be passed to a Bio::DB::GenBank object in order to retrieve the entries corresponding to
       the query.

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::Query::GenBank->new(@args)
        Function: create new query object
        Returns : new query object
        Args    : -db       database (see below for allowable values)
                  -query    query string
                  -mindate  minimum date to retrieve from (YYYY/MM/DD)
                  -maxdate  maximum date to retrieve from (YYYY/MM/DD)
                  -reldate  relative date to retrieve from (days)
                  -datetype date field to use ('edat' or 'mdat')
                  -ids      array ref of gids (overrides query)
                  -maxids   the maximum number of IDs you wish to collect
                            (defaults to 100)

       This method creates a new query object.  Typically you will specify a -db and a -query
       argument, possibly modified by -mindate, -maxdate, or -reldate.  -mindate and -maxdate
       specify minimum and maximum dates for entries you are interested in retrieving, expressed
       in the form YYYY/MM/DD.  -reldate is used to fetch entries that are more recent than the
       indicated number of days.

       If you provide an array reference of IDs in -ids, the query will be ignored and the list
       of IDs will be used when the query is passed to a Bio::DB::GenBank object's
       get_Stream_by_query() method.  A variety of IDs are automatically recognized, including GI
       numbers, Accession numbers, Accession.version numbers and locus names.

       By default, the query will collect only the first 100 IDs and will generate an exception
       if you call the ids() method and the query returned more than that number.  To increase
       this maximum, set -maxids to a number larger than the number of IDs you expect to obtain.
       This only affects the list of IDs you obtain when you call the ids() method, and does not
       affect in any way the number of entries you receive when you generate a SeqIO stream from
       the query.

       -db option values:

         The most commonly used databases are:

             protein
             nucleotide
             nuccore
             nucgss
             nucest
             unigene

         An up to date list of database names supported by NCBI eUtils is
         always available at:
         https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?

         However, note that not all of these databases return datatypes that
         are parsable by Bio::DB::GenBank

   cookie
        Title   : cookie
        Usage   : ($cookie,$querynum) = $db->cookie
        Function: return the NCBI query cookie
        Returns : list of (cookie,querynum)
        Args    : none

       NOTE: this information is used by Bio::DB::GenBank in conjunction with efetch.

   _request_parameters
        Title   : _request_parameters
        Usage   : ($method,$base,@params = $db->_request_parameters
        Function: return information needed to construct the request
        Returns : list of method, url base and key=>value pairs
        Args    : none

   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

   _parse_response
        Title   : _parse_response
        Usage   : $db->_parse_response($content)
        Function: parse out response
        Returns : empty
        Args    : none
        Throws  : 'unparseable output exception'

   _generate_id_string
        Title   : _generate_id_string
        Usage   : $string = $db->_generate_id_string
        Function: joins IDs together in string (possibly implementation-dependent)
        Returns : string of concatenated IDs
        Args    : array ref of ids (normally passed into the constructor)