<![CDATA[
#!/perl/bin/perl
use strict;
use warnings;
use Bio::DB::GenBank;
use Bio::DB::Query::GenBank;
=head1 NAME
querydb.pl - query the GenBank database
=head1 SYNOPSIS
querydb.pl
=head1 DESCRIPTION
querydb.pl looks up a specific query string in the GenBank database to retrieve the
desired sequences. The program then displays the sequence ids and lengths
=head1 AUTHOR
Based on an example from the BioPerl Howto page
=cut
my $seq_obj;
my $stream_obj;
my $query = "Arabidopsis[ORGN] AND topoisomerase[TITL] and 0:3000[SLEN]";
print "Looking up $query in GenBank";
$stream_obj = query_db($query);
print "ID", "\t\t", "Length", "\n";
print "----------", "\t", "------", "\n";
while ($seq_obj = $stream_obj->next_seq) {
printf("%-10s\t%d\n", $seq_obj->display_id, $seq_obj->length);
}
exit(0);
# The query_db function
# This takes the query string and looks up the sequence information
# It returns the resulting stream object obtained from the query.
sub query_db {
my ($query) = @_;
my $query_obj;
my $gb_obj;
my $stream_obj;
$query_obj = Bio::DB::Query::GenBank->new(-db => 'nucleotide',
-query => $query );
$gb_obj = Bio::DB::GenBank->new;
$stream_obj = $gb_obj->get_Stream_by_query($query_obj);
return $stream_obj;
}
]]>