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Bio::DB::Query::GenBank.3pm

NAME

Bio::DB::Query::GenBank - Build a GenBank Entrez Query

SYNOPSIS

    use Bio::DB::Query::GenBank;
    use Bio::DB::GenBank;
 
    my $query_string = 'Oryza[Organism] AND EST[Keyword]';
    my $query = Bio::DB::Query::GenBank->new(-db => 'nucleotide',
                                             -query => $query_string,
                                             -mindate => '2001',
                                             -maxdate => '2002');
 
    print $query->count,"\n";
 
    # get a Genbank database handle
    my $gb = Bio::DB::GenBank->new();
    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]);
 
 

DESCRIPTION

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.

FEEDBACK

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/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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.

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 the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Lincoln Stein

Email lstein@cshl.org

APPENDIX

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 (see below for allowable values)
            -query    query string
            -mindate  minimum date to retrieve from (YYYY/MM/DD)
            -maxdate  maximum date to retrieve from (YYYY/MM/DD)
            -reldate  relative date to retrieve from (days)
            -datetype date field to use ('edat' or 'mdat')
            -ids      array ref of gids (overrides query)
            -maxids   the maximum number of IDs you wish to collect
                      (defaults to 100)
 
 

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 YYYY/MM/DD. -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.

By default, the query will collect only the first 100 IDs and will generate an exception if you call the ids() method and the query returned more than that number. To increase this maximum, set -maxids to a number larger than the number of IDs you expect to obtain. This only affects the list of IDs you obtain when you call the ids() method, and does not affect in any way the number of entries you receive when you generate a SeqIO stream from the query.

-db option values:

   The most commonly used databases are:
 
       protein
       nucleotide
       nuccore
       nucgss
       nucest
       unigene
 
   An up to date list of database names supported by NCBI eUtils is
   always available at:
   http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?
 
   However, note that not all of these databases return datatypes that
   are parsable by Bio::DB::GenBank
 
 

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'
 
 

_generate_id_string

  Title   : _generate_id_string
  Usage   : $string = $db->_generate_id_string
  Function: joins IDs together in string (possibly implementation-dependent)
  Returns : string of concatenated IDs
  Args    : array ref of ids (normally passed into the constructor)