| Bio::DB::QueryI(3pm) | User Contributed Perl Documentation | Bio::DB::QueryI(3pm) |
Bio::DB::QueryI - Object Interface to queryable sequence databases
# 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']);
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.
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
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.
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
Email lstein@cshl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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
| 2020-10-28 | perl v5.30.3 |