Nikki2 | 10 Dec 09:07 2012
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Eutilities and no DocSums returned from NCBI assembly database


Hi,

I'm using 'Bio::DB::EUtilities' in order to retrieve all the names from
'Tracheophyta' that are NCBI's assembly database. However, there are no
DocSums returned for the uid's that match the query. When I try the same
thing using the genome database it works fine.

The script that I used to do the query is at the bottom of this message. The
output I get when running the script is:

Count = 84

--------------------- WARNING ---------------------
MSG: No returned docsums.
---------------------------------------------------

I checked the  <at> ids array and it contains the 84 uids.

My questions are as follows:

1) Is it possible to get DocSums for uids from the NCBI assembly database,
and if yes, how?
2) If not, does anyone have any suggestions how to change my script to get
the species-names that match the uids that are returned?

Thanks a lot!

Nikki

##############################################

#!/bin/perl -w

use Bio::DB::EUtilities;

my $factory = Bio::DB::EUtilities->new(-eutil  => 'esearch',
                                       -db     => 'genome',
				       -email => 'my_email <at> gmail.com',
                                       -term   => 'Tracheophyta[organism]',
                                       -retmax => 5000);

print "Count = ",$factory->get_count,"\n";
my  <at> ids = $factory->get_ids;

my $factory2 = Bio::DB::EUtilities->new(-eutil => 'esummary',
					-email=>'my_email <at> gmail.com',
					-db    => 'genome',
                                        -id    => \ <at> ids,
					ret_max=>5000);

while (my $ds = $factory2->next_DocSum) {
    print "ID: ",$ds->get_id,"\n";
    # flattened mode, iterates through all Item objects
    while (my $item = $ds->next_Item('flattened'))  {
        # not all Items have content, so need to check...
        printf("%-20s:%s\n",$item->get_name,$item->get_content) if
$item->get_content;
   }
    print "\n";
}

--

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