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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',
   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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Please direct usage questions or support issues to the mailing list:

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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AUTHOR - Lincoln Stein



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