eutils fix

use Bio::DB::EUtilities;
 
my (%taxa, @taxa);
my (%names, %idmap);
 
# these are protein ids; nuc ids will work by changing -dbfrom => 'nucleotide',
# (probably)
 
my @ids = qw(1621261 89318838 68536103 20807972 730439);
 
my $factory = Bio::DB::EUtilities->new(-eutil => 'elink',
                                       -db => 'taxonomy',
                                       -email => 'cjfields@bioperl.org',
                                       -dbfrom => 'protein',
                                       -correspondence => 1,
                                       -id => \@ids);
 
# iterate through the LinkSet objects
while (my $ds = $factory->next_LinkSet) {
    $taxa{($ds->get_submitted_ids)[0]} = ($ds->get_ids)[0]
}
 
# don't use a slice when you need all values; if one of the
# ids in the original list is missing, you'll get an undef
# mixed in the array

@taxa = values %taxa; 

$factory->reset_parameters(
        -email => 'cjfields@bioperl.org',
        -eutil => 'esummary',
        -db    => 'taxonomy',
        -id    => \@taxa );

while (my $ds = $factory->next_DocSum) {
    $names{($ds->get_contents_by_name('TaxId'))[0]} = 
    ($ds->get_contents_by_name('ScientificName'))[0];
}
 
foreach my $id (@ids) {
    # again, this assumes all IDs are found, use exists to check
    $idmap{$id} = $names{$taxa{$id}} if exists $taxa{$id};
}