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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : $db = Bio::DB::Query::GenBank->new(@args) Function: create new query object Returns : new query object Args : -db database ('protein' or 'nucleotide') -query query string -mindate minimum date to retrieve from -maxdate maximum date to retrieve from -reldate relative date to retrieve from (days) -datetype date field to use ('edat' or 'mdat') -ids array ref of gids (overrides query)
This method creates a new query object. Typically you will specify a -db and a -query argument, possibly modified by -mindate, -maxdate, or -reldate. -mindate and -maxdate specify minimum and maximum dates for entries you are interested in retrieving, expressed in the form DD/MM/YYYY. -reldate is used to fetch entries that are more recent than the indicated number of days.
If you provide an array reference of IDs in -ids, the query will be ignored and the list of IDs will be used when the query is passed to a Bio::DB::GenBank object's get_Stream_by_query() method. A variety of IDs are automatically recognized, including GI numbers, Accession numbers, Accession.version numbers and locus names.
Title : cookie Usage : ($cookie,$querynum) = $db->cookie Function: return the NCBI query cookie Returns : list of (cookie,querynum) Args : none
NOTE: this information is used by Bio::DB::GenBank in conjunction with efetch.
Title : _request_parameters Usage : ($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
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.
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
Title : query Usage : $query = $db->query([$query]) Function: get/set query string Returns : string Args : (optional) new query string
Title : _parse_response Usage : $db->_parse_response($content) Function: parse out response Returns : empty Args : none Throws : 'unparseable output exception'
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.