Bio::DB::Query::GenBank - Build a GenBank Entrez Query my $query_string = 'Oryza[Organism] AND EST[Keyword]'; my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide', -query=>$query_string, -mindate => '2001', -maxdate => '2002'); my $count = $query->count; my @ids = $query->ids; # get a genbank database handle my $gb = new Bio::DB::GenBank; 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]); 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.

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/MailList.shtml - About the mailing lists

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://bugzilla.bioperl.org/ Email lstein@cshl.org 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 ('protein' or 'nucleotide') -query query string -mindate minimum date to retrieve from -maxdate maximum date to retrieve from -reldate relative date to retrieve from (days) -datetype date field to use ('edat' or 'mdat') -ids array ref of gids (overrides query) 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 DD/MM/YYYY. -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.

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'