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Bio::DB::GDB.3pm

NAME

Bio::DB::GDB - Database object interface to GDB HTTP query

SYNOPSIS

     use Bio::DB::GDB;
 
     $gdb = new Bio::DB::GDB;
 
     $info = $gdb->get_info(-type => 'marker',
                                           -id => 'D1S243'); # Marker name
 
    print "genbank id is ", $info->{'gdbid'},
     "\nprimers are (fwd, rev) ", join(",", @{$info->{'primers'}}), 
     "\nproduct length is ", $info->{'length'}, "\n";
 
 

DESCRIPTION

This class allows connections to the Genome Database (GDB) and queries to retrieve any database objects. See http://www.gdb.org/ or any mirror for details.

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
 
 

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 - Jason Stajich

Email jason@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

ua

  Title   : ua
  Usage   : my $ua = $self->ua or 
            $self->ua($ua)
  Function: Get/Set a LWP::UserAgent for use
  Returns : reference to LWP::UserAgent Object
  Args    : $ua - must be a LWP::UserAgent
 
 

get_params

  Title   : get_params
  Usage   : my %params = $self->get_params($mode)
  Function: Returns key,value pairs to be passed to query
             for mode ('marker', 'gene')
  Returns : a key,value pair hash
  Args    : 'marker' or 'gene' mode for retrieval
 
 

get_info

  Title   : get_info
  Usage   : my $info = $self->get_info(-type => 'marker',
                                       -id   => 'D1S234'); 
  Function: Returns key,value pairs specific
  Returns : a key,value pair hash
  Args    : -type => 'marker' or 'gene' mode for retrieval
            -id   => unique id to query for
 
 

get_request

  Title   : get_request
  Usage   : my $url = $self->get_request
  Function: HTTP::Request
  Returns : 
  Args    : %qualifiers = a hash of qualifiers (ids, format, etc)