Bio::DB::GDB - Database object interface to GDB HTTP query
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";
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.
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
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/
Email jason@bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc)
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.