| 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.
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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.
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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::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
| 2021-08-15 | perl v5.32.1 |